2 See the "run control" section for a working example of the
3 syntax to use when making .mdp entries, with and without detailed
4 documentation for values those entries might take. Everything can
5 be cross-referenced, see the examples there.
7 .. todo:: Make more cross-references.
9 Molecular dynamics parameters (.mdp options)
10 ============================================
17 Default values are given in parentheses, or listed first among
18 choices. The first option in the list is always the default
19 option. Units are given in square brackets. The difference between a
20 dash and an underscore is ignored.
22 A :ref:`sample mdp file <mdp>` is available. This should be
23 appropriate to start a normal simulation. Edit it to suit your
24 specific needs and desires.
32 directories to include in your topology. Format:
33 ``-I/home/john/mylib -I../otherlib``
37 defines to pass to the preprocessor, default is no defines. You can
38 use any defines to control options in your customized topology
39 files. Options that act on existing :ref:`top` file mechanisms
42 ``-DFLEXIBLE`` will use flexible water instead of rigid water
43 into your topology, this can be useful for normal mode analysis.
45 ``-DPOSRES`` will trigger the inclusion of ``posre.itp`` into
46 your topology, used for implementing position restraints.
54 (Despite the name, this list includes algorithms that are not
55 actually integrators over time. :mdp-value:`integrator=steep` and
56 all entries following it are in this category)
60 A leap-frog algorithm for integrating Newton's equations of motion.
64 A velocity Verlet algorithm for integrating Newton's equations
65 of motion. For constant NVE simulations started from
66 corresponding points in the same trajectory, the trajectories
67 are analytically, but not binary, identical to the
68 :mdp-value:`integrator=md` leap-frog integrator. The kinetic
69 energy, which is determined from the whole step velocities and
70 is therefore slightly too high. The advantage of this integrator
71 is more accurate, reversible Nose-Hoover and Parrinello-Rahman
72 coupling integration based on Trotter expansion, as well as
73 (slightly too small) full step velocity output. This all comes
74 at the cost off extra computation, especially with constraints
75 and extra communication in parallel. Note that for nearly all
76 production simulations the :mdp-value:`integrator=md` integrator
79 .. mdp-value:: md-vv-avek
81 A velocity Verlet algorithm identical to
82 :mdp-value:`integrator=md-vv`, except that the kinetic energy is
83 determined as the average of the two half step kinetic energies
84 as in the :mdp-value:`integrator=md` integrator, and this thus
85 more accurate. With Nose-Hoover and/or Parrinello-Rahman
86 coupling this comes with a slight increase in computational
91 An accurate and efficient leap-frog stochastic dynamics
92 integrator. With constraints, coordinates needs to be
93 constrained twice per integration step. Depending on the
94 computational cost of the force calculation, this can take a
95 significant part of the simulation time. The temperature for one
96 or more groups of atoms (:mdp:`tc-grps`) is set with
97 :mdp:`ref-t`, the inverse friction constant for each group is
98 set with :mdp:`tau-t`. The parameters :mdp:`tcoupl` and :mdp:`nsttcouple`
99 are ignored. The random generator is initialized with
100 :mdp:`ld-seed`. When used as a thermostat, an appropriate value
101 for :mdp:`tau-t` is 2 ps, since this results in a friction that
102 is lower than the internal friction of water, while it is high
103 enough to remove excess heat NOTE: temperature deviations decay
104 twice as fast as with a Berendsen thermostat with the same
109 An Euler integrator for Brownian or position Langevin dynamics,
110 the velocity is the force divided by a friction coefficient
111 (:mdp:`bd-fric`) plus random thermal noise (:mdp:`ref-t`). When
112 :mdp:`bd-fric` is 0, the friction coefficient for each particle
113 is calculated as mass/ :mdp:`tau-t`, as for the integrator
114 :mdp-value:`integrator=sd`. The random generator is initialized
119 A steepest descent algorithm for energy minimization. The
120 maximum step size is :mdp:`emstep`, the tolerance is
125 A conjugate gradient algorithm for energy minimization, the
126 tolerance is :mdp:`emtol`. CG is more efficient when a steepest
127 descent step is done every once in a while, this is determined
128 by :mdp:`nstcgsteep`. For a minimization prior to a normal mode
129 analysis, which requires a very high accuracy, |Gromacs| should be
130 compiled in double precision.
132 .. mdp-value:: l-bfgs
134 A quasi-Newtonian algorithm for energy minimization according to
135 the low-memory Broyden-Fletcher-Goldfarb-Shanno approach. In
136 practice this seems to converge faster than Conjugate Gradients,
137 but due to the correction steps necessary it is not (yet)
142 Normal mode analysis is performed on the structure in the :ref:`tpr`
143 file. |Gromacs| should be compiled in double precision.
147 Test particle insertion. The last molecule in the topology is
148 the test particle. A trajectory must be provided to ``mdrun
149 -rerun``. This trajectory should not contain the molecule to be
150 inserted. Insertions are performed :mdp:`nsteps` times in each
151 frame at random locations and with random orientiations of the
152 molecule. When :mdp:`nstlist` is larger than one,
153 :mdp:`nstlist` insertions are performed in a sphere with radius
154 :mdp:`rtpi` around a the same random location using the same
155 pair list. Since pair list construction is expensive,
156 one can perform several extra insertions with the same list
157 almost for free. The random seed is set with
158 :mdp:`ld-seed`. The temperature for the Boltzmann weighting is
159 set with :mdp:`ref-t`, this should match the temperature of the
160 simulation of the original trajectory. Dispersion correction is
161 implemented correctly for TPI. All relevant quantities are
162 written to the file specified with ``mdrun -tpi``. The
163 distribution of insertion energies is written to the file
164 specified with ``mdrun -tpid``. No trajectory or energy file is
165 written. Parallel TPI gives identical results to single-node
166 TPI. For charged molecules, using PME with a fine grid is most
167 accurate and also efficient, since the potential in the system
168 only needs to be calculated once per frame.
172 Test particle insertion into a predefined cavity location. The
173 procedure is the same as for :mdp-value:`integrator=tpi`, except
174 that one coordinate extra is read from the trajectory, which is
175 used as the insertion location. The molecule to be inserted
176 should be centered at 0,0,0. |Gromacs| does not do this for you,
177 since for different situations a different way of centering
178 might be optimal. Also :mdp:`rtpi` sets the radius for the
179 sphere around this location. Neighbor searching is done only
180 once per frame, :mdp:`nstlist` is not used. Parallel
181 :mdp-value:`integrator=tpic` gives identical results to
182 single-rank :mdp-value:`integrator=tpic`.
186 Enable MiMiC QM/MM coupling to run hybrid molecular dynamics.
187 Keey in mind that its required to launch CPMD compiled with MiMiC as well.
188 In this mode all options regarding integration (T-coupling, P-coupling,
189 timestep and number of steps) are ignored as CPMD will do the integration
190 instead. Options related to forces computation (cutoffs, PME parameters,
191 etc.) are working as usual. Atom selection to define QM atoms is read
192 from :mdp:`QMMM-grps`
197 starting time for your run (only makes sense for time-based
203 time step for integration (only makes sense for time-based
209 maximum number of steps to integrate or minimize, -1 is no
215 The starting step. The time at step i in a run is
216 calculated as: t = :mdp:`tinit` + :mdp:`dt` *
217 (:mdp:`init-step` + i). The free-energy lambda is calculated
218 as: lambda = :mdp:`init-lambda` + :mdp:`delta-lambda` *
219 (:mdp:`init-step` + i). Also non-equilibrium MD parameters can
220 depend on the step number. Thus for exact restarts or redoing
221 part of a run it might be necessary to set :mdp:`init-step` to
222 the step number of the restart frame. :ref:`gmx convert-tpr`
223 does this automatically.
225 .. mdp:: simulation-part
228 A simulation can consist of multiple parts, each of which has
229 a part number. This option specifies what that number will
230 be, which helps keep track of parts that are logically the
231 same simulation. This option is generally useful to set only
232 when coping with a crashed simulation where files were lost.
238 Evaluate all forces at every integration step.
242 Use a multiple timing-stepping integrator to evaluate some forces, as specified
243 by :mdp:`mts-level2-forces` every :mdp:`mts-level2-factor` integration
244 steps. All other forces are evaluated at every step. MTS is currently
245 only supported with :mdp-value:`integrator=md`.
250 The number of levels for the multiple time-stepping scheme.
251 Currently only 2 is supported.
253 .. mdp:: mts-level2-forces
255 (longrange-nonbonded nonbonded pair dihedral)
256 A list of force groups that will be evaluated only every
257 :mdp:`mts-level2-factor` steps. Supported entries are:
258 ``longrange-nonbonded``, ``nonbonded``, ``pair``, ``dihedral``, ``angle``,
259 ``pull`` and ``awh``. With ``pair`` the listed pair forces (such as 1-4)
260 are selected. With ``dihedral`` all dihedrals are selected, including cmap.
261 All other forces, including all restraints, are evaluated and
262 integrated every step. When PME or Ewald is used for electrostatics
263 and/or LJ interactions, ``longrange-nonbonded`` has to be entered here.
264 The default value should work well for most standard atomistic simulations
265 and in particular for replacing virtual site treatment for increasing
268 .. mdp:: mts-level2-factor
271 Interval for computing the forces in level 2 of the multiple time-stepping
276 .. mdp-value:: Linear
278 Remove center of mass translational velocity
280 .. mdp-value:: Angular
282 Remove center of mass translational and rotational velocity
284 .. mdp-value:: Linear-acceleration-correction
286 Remove center of mass translational velocity. Correct the center of
287 mass position assuming linear acceleration over :mdp:`nstcomm` steps.
288 This is useful for cases where an acceleration is expected on the
289 center of mass which is nearly constant over :mdp:`nstcomm` steps.
290 This can occur for example when pulling on a group using an absolute
295 No restriction on the center of mass motion
300 frequency for center of mass motion removal
304 group(s) for center of mass motion removal, default is the whole
313 (0) [amu ps\ :sup:`-1`]
314 Brownian dynamics friction coefficient. When :mdp:`bd-fric` is 0,
315 the friction coefficient for each particle is calculated as mass/
321 used to initialize random generator for thermal noise for
322 stochastic and Brownian dynamics. When :mdp:`ld-seed` is set to -1,
323 a pseudo random seed is used. When running BD or SD on multiple
324 processors, each processor uses a seed equal to :mdp:`ld-seed` plus
325 the processor number.
333 (10.0) [kJ mol\ :sup:`-1` nm\ :sup:`-1`]
334 the minimization is converged when the maximum force is smaller
345 frequency of performing 1 steepest descent step while doing
346 conjugate gradient energy minimization.
351 Number of correction steps to use for L-BFGS minimization. A higher
352 number is (at least theoretically) more accurate, but slower.
355 Shell Molecular Dynamics
356 ^^^^^^^^^^^^^^^^^^^^^^^^
358 When shells or flexible constraints are present in the system the
359 positions of the shells and the lengths of the flexible constraints
360 are optimized at every time step until either the RMS force on the
361 shells and constraints is less than :mdp:`emtol`, or a maximum number
362 of iterations :mdp:`niter` has been reached. Minimization is converged
363 when the maximum force is smaller than :mdp:`emtol`. For shell MD this
364 value should be 1.0 at most.
369 maximum number of iterations for optimizing the shell positions and
370 the flexible constraints.
375 the step size for optimizing the flexible constraints. Should be
376 chosen as mu/(d2V/dq2) where mu is the reduced mass of two
377 particles in a flexible constraint and d2V/dq2 is the second
378 derivative of the potential in the constraint direction. Hopefully
379 this number does not differ too much between the flexible
380 constraints, as the number of iterations and thus the runtime is
381 very sensitive to fcstep. Try several values!
384 Test particle insertion
385 ^^^^^^^^^^^^^^^^^^^^^^^
390 the test particle insertion radius, see integrators
391 :mdp-value:`integrator=tpi` and :mdp-value:`integrator=tpic`
400 number of steps that elapse between writing coordinates to the output
401 trajectory file (:ref:`trr`), the last coordinates are always written
402 unless 0, which means coordinates are not written into the trajectory
408 number of steps that elapse between writing velocities to the output
409 trajectory file (:ref:`trr`), the last velocities are always written
410 unless 0, which means velocities are not written into the trajectory
416 number of steps that elapse between writing forces to the output
417 trajectory file (:ref:`trr`), the last forces are always written,
418 unless 0, which means forces are not written into the trajectory
424 number of steps that elapse between writing energies to the log
425 file, the last energies are always written.
427 .. mdp:: nstcalcenergy
430 number of steps that elapse between calculating the energies, 0 is
431 never. This option is only relevant with dynamics. This option affects the
432 performance in parallel simulations, because calculating energies
433 requires global communication between all processes which can
434 become a bottleneck at high parallelization.
439 number of steps that elapse between writing energies to energy file,
440 the last energies are always written, should be a multiple of
441 :mdp:`nstcalcenergy`. Note that the exact sums and fluctuations
442 over all MD steps modulo :mdp:`nstcalcenergy` are stored in the
443 energy file, so :ref:`gmx energy` can report exact energy averages
444 and fluctuations also when :mdp:`nstenergy` > 1
446 .. mdp:: nstxout-compressed
449 number of steps that elapse between writing position coordinates
450 using lossy compression (:ref:`xtc` file), 0 for not writing
451 compressed coordinates output.
453 .. mdp:: compressed-x-precision
456 precision with which to write to the compressed trajectory file
458 .. mdp:: compressed-x-grps
460 group(s) to write to the compressed trajectory file, by default the
461 whole system is written (if :mdp:`nstxout-compressed` > 0)
465 group(s) for which to write to write short-ranged non-bonded
466 potential energies to the energy file (not supported on GPUs)
472 .. mdp:: cutoff-scheme
474 .. mdp-value:: Verlet
476 Generate a pair list with buffering. The buffer size is
477 automatically set based on :mdp:`verlet-buffer-tolerance`,
478 unless this is set to -1, in which case :mdp:`rlist` will be
483 Generate a pair list for groups of atoms, corresponding
484 to the charge groups in the topology. This option is no longer
493 Frequency to update the neighbor list. When dynamics and
494 :mdp:`verlet-buffer-tolerance` set, :mdp:`nstlist` is actually
495 a minimum value and :ref:`gmx mdrun` might increase it, unless
496 it is set to 1. With parallel simulations and/or non-bonded
497 force calculation on the GPU, a value of 20 or 40 often gives
498 the best performance.
502 The neighbor list is only constructed once and never
503 updated. This is mainly useful for vacuum simulations in which
504 all particles see each other. But vacuum simulations are
505 (temporarily) not supported.
515 Use periodic boundary conditions in all directions.
519 Use no periodic boundary conditions, ignore the box. To simulate
520 without cut-offs, set all cut-offs and :mdp:`nstlist` to 0. For
521 best performance without cut-offs on a single MPI rank, set
522 :mdp:`nstlist` to zero and :mdp-value:`ns-type=simple`.
526 Use periodic boundary conditions in x and y directions
527 only. This works only with :mdp-value:`ns-type=grid` and can be used
528 in combination with walls_. Without walls or with only one wall
529 the system size is infinite in the z direction. Therefore
530 pressure coupling or Ewald summation methods can not be
531 used. These disadvantages do not apply when two walls are used.
533 .. mdp:: periodic-molecules
537 molecules are finite, fast molecular PBC can be used
541 for systems with molecules that couple to themselves through the
542 periodic boundary conditions, this requires a slower PBC
543 algorithm and molecules are not made whole in the output
545 .. mdp:: verlet-buffer-tolerance
547 (0.005) [kJ mol\ :sup:`-1` ps\ :sup:`-1`]
549 Used when performing a simulation with dynamics. This sets
550 the maximum allowed error for pair interactions per particle caused
551 by the Verlet buffer, which indirectly sets :mdp:`rlist`. As both
552 :mdp:`nstlist` and the Verlet buffer size are fixed (for
553 performance reasons), particle pairs not in the pair list can
554 occasionally get within the cut-off distance during
555 :mdp:`nstlist` -1 steps. This causes very small jumps in the
556 energy. In a constant-temperature ensemble, these very small energy
557 jumps can be estimated for a given cut-off and :mdp:`rlist`. The
558 estimate assumes a homogeneous particle distribution, hence the
559 errors might be slightly underestimated for multi-phase
560 systems. (See the `reference manual`_ for details). For longer
561 pair-list life-time (:mdp:`nstlist` -1) * :mdp:`dt` the buffer is
562 overestimated, because the interactions between particles are
563 ignored. Combined with cancellation of errors, the actual drift of
564 the total energy is usually one to two orders of magnitude
565 smaller. Note that the generated buffer size takes into account
566 that the |Gromacs| pair-list setup leads to a reduction in the
567 drift by a factor 10, compared to a simple particle-pair based
568 list. Without dynamics (energy minimization etc.), the buffer is 5%
569 of the cut-off. For NVE simulations the initial temperature is
570 used, unless this is zero, in which case a buffer of 10% is
571 used. For NVE simulations the tolerance usually needs to be lowered
572 to achieve proper energy conservation on the nanosecond time
573 scale. To override the automated buffer setting, use
574 :mdp:`verlet-buffer-tolerance` =-1 and set :mdp:`rlist` manually.
579 Cut-off distance for the short-range neighbor list. With dynamics,
580 this is by default set by the :mdp:`verlet-buffer-tolerance` option
581 and the value of :mdp:`rlist` is ignored. Without dynamics, this
582 is by default set to the maximum cut-off plus 5% buffer, except
583 for test particle insertion, where the buffer is managed exactly
584 and automatically. For NVE simulations, where the automated
585 setting is not possible, the advised procedure is to run :ref:`gmx grompp`
586 with an NVT setup with the expected temperature and copy the resulting
587 value of :mdp:`rlist` to the NVE setup.
595 .. mdp-value:: Cut-off
597 Plain cut-off with pair list radius :mdp:`rlist` and
598 Coulomb cut-off :mdp:`rcoulomb`, where :mdp:`rlist` >=
603 Classical Ewald sum electrostatics. The real-space cut-off
604 :mdp:`rcoulomb` should be equal to :mdp:`rlist`. Use *e.g.*
605 :mdp:`rlist` =0.9, :mdp:`rcoulomb` =0.9. The highest magnitude
606 of wave vectors used in reciprocal space is controlled by
607 :mdp:`fourierspacing`. The relative accuracy of
608 direct/reciprocal space is controlled by :mdp:`ewald-rtol`.
610 NOTE: Ewald scales as O(N\ :sup:`3/2`) and is thus extremely slow for
611 large systems. It is included mainly for reference - in most
612 cases PME will perform much better.
616 Fast smooth Particle-Mesh Ewald (SPME) electrostatics. Direct
617 space is similar to the Ewald sum, while the reciprocal part is
618 performed with FFTs. Grid dimensions are controlled with
619 :mdp:`fourierspacing` and the interpolation order with
620 :mdp:`pme-order`. With a grid spacing of 0.1 nm and cubic
621 interpolation the electrostatic forces have an accuracy of
622 2-3*10\ :sup:`-4`. Since the error from the vdw-cutoff is larger than
623 this you might try 0.15 nm. When running in parallel the
624 interpolation parallelizes better than the FFT, so try
625 decreasing grid dimensions while increasing interpolation.
627 .. mdp-value:: P3M-AD
629 Particle-Particle Particle-Mesh algorithm with analytical
630 derivative for for long range electrostatic interactions. The
631 method and code is identical to SPME, except that the influence
632 function is optimized for the grid. This gives a slight increase
635 .. mdp-value:: Reaction-Field
637 Reaction field electrostatics with Coulomb cut-off
638 :mdp:`rcoulomb`, where :mdp:`rlist` >= :mdp:`rvdw`. The
639 dielectric constant beyond the cut-off is
640 :mdp:`epsilon-rf`. The dielectric constant can be set to
641 infinity by setting :mdp:`epsilon-rf` =0.
645 Currently unsupported.
646 :ref:`gmx mdrun` will now expect to find a file ``table.xvg``
647 with user-defined potential functions for repulsion, dispersion
648 and Coulomb. When pair interactions are present, :ref:`gmx
649 mdrun` also expects to find a file ``tablep.xvg`` for the pair
650 interactions. When the same interactions should be used for
651 non-bonded and pair interactions the user can specify the same
652 file name for both table files. These files should contain 7
653 columns: the ``x`` value, ``f(x)``, ``-f'(x)``, ``g(x)``,
654 ``-g'(x)``, ``h(x)``, ``-h'(x)``, where ``f(x)`` is the Coulomb
655 function, ``g(x)`` the dispersion function and ``h(x)`` the
656 repulsion function. When :mdp:`vdwtype` is not set to User the
657 values for ``g``, ``-g'``, ``h`` and ``-h'`` are ignored. For
658 the non-bonded interactions ``x`` values should run from 0 to
659 the largest cut-off distance + :mdp:`table-extension` and
660 should be uniformly spaced. For the pair interactions the table
661 length in the file will be used. The optimal spacing, which is
662 used for non-user tables, is ``0.002 nm`` when you run in mixed
663 precision or ``0.0005 nm`` when you run in double precision. The
664 function value at ``x=0`` is not important. More information is
665 in the printed manual.
667 .. mdp-value:: PME-Switch
669 Currently unsupported.
670 A combination of PME and a switch function for the direct-space
671 part (see above). :mdp:`rcoulomb` is allowed to be smaller than
674 .. mdp-value:: PME-User
676 Currently unsupported.
677 A combination of PME and user tables (see
678 above). :mdp:`rcoulomb` is allowed to be smaller than
679 :mdp:`rlist`. The PME mesh contribution is subtracted from the
680 user table by :ref:`gmx mdrun`. Because of this subtraction the
681 user tables should contain about 10 decimal places.
683 .. mdp-value:: PME-User-Switch
685 Currently unsupported.
686 A combination of PME-User and a switching function (see
687 above). The switching function is applied to final
688 particle-particle interaction, *i.e.* both to the user supplied
689 function and the PME Mesh correction part.
691 .. mdp:: coulomb-modifier
693 .. mdp-value:: Potential-shift
695 Shift the Coulomb potential by a constant such that it is zero
696 at the cut-off. This makes the potential the integral of the
697 force. Note that this does not affect the forces or the
702 Use an unmodified Coulomb potential. This can be useful
703 when comparing energies with those computed with other software.
705 .. mdp:: rcoulomb-switch
708 where to start switching the Coulomb potential, only relevant
709 when force or potential switching is used
714 The distance for the Coulomb cut-off. Note that with PME this value
715 can be increased by the PME tuning in :ref:`gmx mdrun` along with
716 the PME grid spacing.
721 The relative dielectric constant. A value of 0 means infinity.
726 The relative dielectric constant of the reaction field. This
727 is only used with reaction-field electrostatics. A value of 0
736 .. mdp-value:: Cut-off
738 Plain cut-off with pair list radius :mdp:`rlist` and VdW
739 cut-off :mdp:`rvdw`, where :mdp:`rlist` >= :mdp:`rvdw`.
743 Fast smooth Particle-mesh Ewald (SPME) for VdW interactions. The
744 grid dimensions are controlled with :mdp:`fourierspacing` in
745 the same way as for electrostatics, and the interpolation order
746 is controlled with :mdp:`pme-order`. The relative accuracy of
747 direct/reciprocal space is controlled by :mdp:`ewald-rtol-lj`,
748 and the specific combination rules that are to be used by the
749 reciprocal routine are set using :mdp:`lj-pme-comb-rule`.
753 This functionality is deprecated and replaced by using
754 :mdp-value:`vdwtype=Cut-off` with :mdp-value:`vdw-modifier=Force-switch`.
755 The LJ (not Buckingham) potential is decreased over the whole range and
756 the forces decay smoothly to zero between :mdp:`rvdw-switch` and
759 .. mdp-value:: Switch
761 This functionality is deprecated and replaced by using
762 :mdp-value:`vdwtype=Cut-off` with :mdp-value:`vdw-modifier=Potential-switch`.
763 The LJ (not Buckingham) potential is normal out to :mdp:`rvdw-switch`, after
764 which it is switched off to reach zero at :mdp:`rvdw`. Both the
765 potential and force functions are continuously smooth, but be
766 aware that all switch functions will give rise to a bulge
767 (increase) in the force (since we are switching the
772 Currently unsupported.
773 See user for :mdp:`coulombtype`. The function value at zero is
774 not important. When you want to use LJ correction, make sure
775 that :mdp:`rvdw` corresponds to the cut-off in the user-defined
776 function. When :mdp:`coulombtype` is not set to User the values
777 for the ``f`` and ``-f'`` columns are ignored.
779 .. mdp:: vdw-modifier
781 .. mdp-value:: Potential-shift
783 Shift the Van der Waals potential by a constant such that it is
784 zero at the cut-off. This makes the potential the integral of
785 the force. Note that this does not affect the forces or the
790 Use an unmodified Van der Waals potential. This can be useful
791 when comparing energies with those computed with other software.
793 .. mdp-value:: Force-switch
795 Smoothly switches the forces to zero between :mdp:`rvdw-switch`
796 and :mdp:`rvdw`. This shifts the potential shift over the whole
797 range and switches it to zero at the cut-off. Note that this is
798 more expensive to calculate than a plain cut-off and it is not
799 required for energy conservation, since Potential-shift
800 conserves energy just as well.
802 .. mdp-value:: Potential-switch
804 Smoothly switches the potential to zero between
805 :mdp:`rvdw-switch` and :mdp:`rvdw`. Note that this introduces
806 articifically large forces in the switching region and is much
807 more expensive to calculate. This option should only be used if
808 the force field you are using requires this.
813 where to start switching the LJ force and possibly the potential,
814 only relevant when force or potential switching is used
819 distance for the LJ or Buckingham cut-off
825 don't apply any correction
827 .. mdp-value:: EnerPres
829 apply long range dispersion corrections for Energy and Pressure
833 apply long range dispersion corrections for Energy only
839 .. mdp:: table-extension
842 Extension of the non-bonded potential lookup tables beyond the
843 largest cut-off distance. With actual non-bonded interactions
844 the tables are never accessed beyond the cut-off. But a longer
845 table length might be needed for the 1-4 interactions, which
846 are always tabulated irrespective of the use of tables for
847 the non-bonded interactions.
849 .. mdp:: energygrp-table
851 Currently unsupported.
852 When user tables are used for electrostatics and/or VdW, here one
853 can give pairs of energy groups for which seperate user tables
854 should be used. The two energy groups will be appended to the table
855 file name, in order of their definition in :mdp:`energygrps`,
856 seperated by underscores. For example, if ``energygrps = Na Cl
857 Sol`` and ``energygrp-table = Na Na Na Cl``, :ref:`gmx mdrun` will
858 read ``table_Na_Na.xvg`` and ``table_Na_Cl.xvg`` in addition to the
859 normal ``table.xvg`` which will be used for all other energy group
866 .. mdp:: fourierspacing
869 For ordinary Ewald, the ratio of the box dimensions and the spacing
870 determines a lower bound for the number of wave vectors to use in
871 each (signed) direction. For PME and P3M, that ratio determines a
872 lower bound for the number of Fourier-space grid points that will
873 be used along that axis. In all cases, the number for each
874 direction can be overridden by entering a non-zero value for that
875 :mdp:`fourier-nx` direction. For optimizing the relative load of
876 the particle-particle interactions and the mesh part of PME, it is
877 useful to know that the accuracy of the electrostatics remains
878 nearly constant when the Coulomb cut-off and the PME grid spacing
879 are scaled by the same factor. Note that this spacing can be scaled
880 up along with :mdp:`rcoulomb` by the PME tuning in :ref:`gmx mdrun`.
887 Highest magnitude of wave vectors in reciprocal space when using Ewald.
888 Grid size when using PME or P3M. These values override
889 :mdp:`fourierspacing` per direction. The best choice is powers of
890 2, 3, 5 and 7. Avoid large primes. Note that these grid sizes can
891 be reduced along with scaling up :mdp:`rcoulomb` by the PME tuning
897 Interpolation order for PME. 4 equals cubic interpolation. You
898 might try 6/8/10 when running in parallel and simultaneously
899 decrease grid dimension.
904 The relative strength of the Ewald-shifted direct potential at
905 :mdp:`rcoulomb` is given by :mdp:`ewald-rtol`. Decreasing this
906 will give a more accurate direct sum, but then you need more wave
907 vectors for the reciprocal sum.
909 .. mdp:: ewald-rtol-lj
912 When doing PME for VdW-interactions, :mdp:`ewald-rtol-lj` is used
913 to control the relative strength of the dispersion potential at
914 :mdp:`rvdw` in the same way as :mdp:`ewald-rtol` controls the
915 electrostatic potential.
917 .. mdp:: lj-pme-comb-rule
920 The combination rules used to combine VdW-parameters in the
921 reciprocal part of LJ-PME. Geometric rules are much faster than
922 Lorentz-Berthelot and usually the recommended choice, even when the
923 rest of the force field uses the Lorentz-Berthelot rules.
925 .. mdp-value:: Geometric
927 Apply geometric combination rules
929 .. mdp-value:: Lorentz-Berthelot
931 Apply Lorentz-Berthelot combination rules
933 .. mdp:: ewald-geometry
937 The Ewald sum is performed in all three dimensions.
941 The reciprocal sum is still performed in 3D, but a force and
942 potential correction applied in the ``z`` dimension to produce a
943 pseudo-2D summation. If your system has a slab geometry in the
944 ``x-y`` plane you can try to increase the ``z``-dimension of the box
945 (a box height of 3 times the slab height is usually ok) and use
948 .. mdp:: epsilon-surface
951 This controls the dipole correction to the Ewald summation in
952 3D. The default value of zero means it is turned off. Turn it on by
953 setting it to the value of the relative permittivity of the
954 imaginary surface around your infinite system. Be careful - you
955 shouldn't use this if you have free mobile charges in your
956 system. This value does not affect the slab 3DC variant of the long
967 No temperature coupling.
969 .. mdp-value:: berendsen
971 Temperature coupling with a Berendsen thermostat to a bath with
972 temperature :mdp:`ref-t`, with time constant
973 :mdp:`tau-t`. Several groups can be coupled separately, these
974 are specified in the :mdp:`tc-grps` field separated by spaces.
976 .. mdp-value:: nose-hoover
978 Temperature coupling using a Nose-Hoover extended ensemble. The
979 reference temperature and coupling groups are selected as above,
980 but in this case :mdp:`tau-t` controls the period of the
981 temperature fluctuations at equilibrium, which is slightly
982 different from a relaxation time. For NVT simulations the
983 conserved energy quantity is written to the energy and log files.
985 .. mdp-value:: andersen
987 Temperature coupling by randomizing a fraction of the particle velocities
988 at each timestep. Reference temperature and coupling groups are
989 selected as above. :mdp:`tau-t` is the average time between
990 randomization of each molecule. Inhibits particle dynamics
991 somewhat, but little or no ergodicity issues. Currently only
992 implemented with velocity Verlet, and not implemented with
995 .. mdp-value:: andersen-massive
997 Temperature coupling by randomizing velocities of all particles at
998 infrequent timesteps. Reference temperature and coupling groups are
999 selected as above. :mdp:`tau-t` is the time between
1000 randomization of all molecules. Inhibits particle dynamics
1001 somewhat, but little or no ergodicity issues. Currently only
1002 implemented with velocity Verlet.
1004 .. mdp-value:: v-rescale
1006 Temperature coupling using velocity rescaling with a stochastic
1007 term (JCP 126, 014101). This thermostat is similar to Berendsen
1008 coupling, with the same scaling using :mdp:`tau-t`, but the
1009 stochastic term ensures that a proper canonical ensemble is
1010 generated. The random seed is set with :mdp:`ld-seed`. This
1011 thermostat works correctly even for :mdp:`tau-t` =0. For NVT
1012 simulations the conserved energy quantity is written to the
1013 energy and log file.
1018 The frequency for coupling the temperature. The default value of -1
1019 sets :mdp:`nsttcouple` equal to 10, or fewer steps if required
1020 for accurate integration. Note that the default value is not 1
1021 because additional computation and communication is required for
1022 obtaining the kinetic energy. For velocity
1023 Verlet integrators :mdp:`nsttcouple` is set to 1.
1025 .. mdp:: nh-chain-length
1028 The number of chained Nose-Hoover thermostats for velocity Verlet
1029 integrators, the leap-frog :mdp-value:`integrator=md` integrator
1030 only supports 1. Data for the NH chain variables is not printed
1031 to the :ref:`edr` file by default, but can be turned on with the
1032 :mdp:`print-nose-hoover-chain-variables` option.
1034 .. mdp:: print-nose-hoover-chain-variables
1038 Do not store Nose-Hoover chain variables in the energy file.
1042 Store all positions and velocities of the Nose-Hoover chain
1047 groups to couple to separate temperature baths
1052 time constant for coupling (one for each group in
1053 :mdp:`tc-grps`), -1 means no temperature coupling
1058 reference temperature for coupling (one for each group in
1069 No pressure coupling. This means a fixed box size.
1071 .. mdp-value:: Berendsen
1073 Exponential relaxation pressure coupling with time constant
1074 :mdp:`tau-p`. The box is scaled every :mdp:`nstpcouple` steps. It has been
1075 argued that this does not yield a correct thermodynamic
1076 ensemble, but it is the most efficient way to scale a box at the
1079 .. mdp-value:: C-rescale
1081 Exponential relaxation pressure coupling with time constant
1082 :mdp:`tau-p`, including a stochastic term to enforce correct
1083 volume fluctuations. The box is scaled every :mdp:`nstpcouple`
1084 steps. It can be used for both equilibration and production.
1086 .. mdp-value:: Parrinello-Rahman
1088 Extended-ensemble pressure coupling where the box vectors are
1089 subject to an equation of motion. The equation of motion for the
1090 atoms is coupled to this. No instantaneous scaling takes
1091 place. As for Nose-Hoover temperature coupling the time constant
1092 :mdp:`tau-p` is the period of pressure fluctuations at
1093 equilibrium. This is probably a better method when you want to
1094 apply pressure scaling during data collection, but beware that
1095 you can get very large oscillations if you are starting from a
1096 different pressure. For simulations where the exact fluctations
1097 of the NPT ensemble are important, or if the pressure coupling
1098 time is very short it may not be appropriate, as the previous
1099 time step pressure is used in some steps of the |Gromacs|
1100 implementation for the current time step pressure.
1104 Martyna-Tuckerman-Tobias-Klein implementation, only useable with
1105 :mdp-value:`integrator=md-vv` or :mdp-value:`integrator=md-vv-avek`, very similar to
1106 Parrinello-Rahman. As for Nose-Hoover temperature coupling the
1107 time constant :mdp:`tau-p` is the period of pressure
1108 fluctuations at equilibrium. This is probably a better method
1109 when you want to apply pressure scaling during data collection,
1110 but beware that you can get very large oscillations if you are
1111 starting from a different pressure. Currently (as of version
1112 5.1), it only supports isotropic scaling, and only works without
1117 Specifies the kind of isotropy of the pressure coupling used. Each
1118 kind takes one or more values for :mdp:`compressibility` and
1119 :mdp:`ref-p`. Only a single value is permitted for :mdp:`tau-p`.
1121 .. mdp-value:: isotropic
1123 Isotropic pressure coupling with time constant
1124 :mdp:`tau-p`. One value each for :mdp:`compressibility` and
1125 :mdp:`ref-p` is required.
1127 .. mdp-value:: semiisotropic
1129 Pressure coupling which is isotropic in the ``x`` and ``y``
1130 direction, but different in the ``z`` direction. This can be
1131 useful for membrane simulations. Two values each for
1132 :mdp:`compressibility` and :mdp:`ref-p` are required, for
1133 ``x/y`` and ``z`` directions respectively.
1135 .. mdp-value:: anisotropic
1137 Same as before, but 6 values are needed for ``xx``, ``yy``, ``zz``,
1138 ``xy/yx``, ``xz/zx`` and ``yz/zy`` components,
1139 respectively. When the off-diagonal compressibilities are set to
1140 zero, a rectangular box will stay rectangular. Beware that
1141 anisotropic scaling can lead to extreme deformation of the
1144 .. mdp-value:: surface-tension
1146 Surface tension coupling for surfaces parallel to the
1147 xy-plane. Uses normal pressure coupling for the ``z``-direction,
1148 while the surface tension is coupled to the ``x/y`` dimensions of
1149 the box. The first :mdp:`ref-p` value is the reference surface
1150 tension times the number of surfaces ``bar nm``, the second
1151 value is the reference ``z``-pressure ``bar``. The two
1152 :mdp:`compressibility` values are the compressibility in the
1153 ``x/y`` and ``z`` direction respectively. The value for the
1154 ``z``-compressibility should be reasonably accurate since it
1155 influences the convergence of the surface-tension, it can also
1156 be set to zero to have a box with constant height.
1161 The frequency for coupling the pressure. The default value of -1
1162 sets :mdp:`nstpcouple` equal to 10, or fewer steps if required
1163 for accurate integration. Note that the default value is not 1
1164 because additional computation and communication is required for
1165 obtaining the virial. For velocity
1166 Verlet integrators :mdp:`nstpcouple` is set to 1.
1171 The time constant for pressure coupling (one value for all
1174 .. mdp:: compressibility
1177 The compressibility (NOTE: this is now really in bar\ :sup:`-1`) For water at 1
1178 atm and 300 K the compressibility is 4.5e-5 bar\ :sup:`-1`. The number of
1179 required values is implied by :mdp:`pcoupltype`.
1184 The reference pressure for coupling. The number of required values
1185 is implied by :mdp:`pcoupltype`.
1187 .. mdp:: refcoord-scaling
1191 The reference coordinates for position restraints are not
1192 modified. Note that with this option the virial and pressure
1193 might be ill defined, see :ref:`here <reference-manual-position-restraints>`
1198 The reference coordinates are scaled with the scaling matrix of
1199 the pressure coupling.
1203 Scale the center of mass of the reference coordinates with the
1204 scaling matrix of the pressure coupling. The vectors of each
1205 reference coordinate to the center of mass are not scaled. Only
1206 one COM is used, even when there are multiple molecules with
1207 position restraints. For calculating the COM of the reference
1208 coordinates in the starting configuration, periodic boundary
1209 conditions are not taken into account. Note that with this option
1210 the virial and pressure might be ill defined, see
1211 :ref:`here <reference-manual-position-restraints>` for more details.
1217 Simulated annealing is controlled separately for each temperature
1218 group in |Gromacs|. The reference temperature is a piecewise linear
1219 function, but you can use an arbitrary number of points for each
1220 group, and choose either a single sequence or a periodic behaviour for
1221 each group. The actual annealing is performed by dynamically changing
1222 the reference temperature used in the thermostat algorithm selected,
1223 so remember that the system will usually not instantaneously reach the
1224 reference temperature!
1228 Type of annealing for each temperature group
1232 No simulated annealing - just couple to reference temperature value.
1234 .. mdp-value:: single
1236 A single sequence of annealing points. If your simulation is
1237 longer than the time of the last point, the temperature will be
1238 coupled to this constant value after the annealing sequence has
1239 reached the last time point.
1241 .. mdp-value:: periodic
1243 The annealing will start over at the first reference point once
1244 the last reference time is reached. This is repeated until the
1247 .. mdp:: annealing-npoints
1249 A list with the number of annealing reference/control points used
1250 for each temperature group. Use 0 for groups that are not
1251 annealed. The number of entries should equal the number of
1254 .. mdp:: annealing-time
1256 List of times at the annealing reference/control points for each
1257 group. If you are using periodic annealing, the times will be used
1258 modulo the last value, *i.e.* if the values are 0, 5, 10, and 15,
1259 the coupling will restart at the 0ps value after 15ps, 30ps, 45ps,
1260 etc. The number of entries should equal the sum of the numbers
1261 given in :mdp:`annealing-npoints`.
1263 .. mdp:: annealing-temp
1265 List of temperatures at the annealing reference/control points for
1266 each group. The number of entries should equal the sum of the
1267 numbers given in :mdp:`annealing-npoints`.
1269 Confused? OK, let's use an example. Assume you have two temperature
1270 groups, set the group selections to ``annealing = single periodic``,
1271 the number of points of each group to ``annealing-npoints = 3 4``, the
1272 times to ``annealing-time = 0 3 6 0 2 4 6`` and finally temperatures
1273 to ``annealing-temp = 298 280 270 298 320 320 298``. The first group
1274 will be coupled to 298K at 0ps, but the reference temperature will
1275 drop linearly to reach 280K at 3ps, and then linearly between 280K and
1276 270K from 3ps to 6ps. After this is stays constant, at 270K. The
1277 second group is coupled to 298K at 0ps, it increases linearly to 320K
1278 at 2ps, where it stays constant until 4ps. Between 4ps and 6ps it
1279 decreases to 298K, and then it starts over with the same pattern
1280 again, *i.e.* rising linearly from 298K to 320K between 6ps and
1281 8ps. Check the summary printed by :ref:`gmx grompp` if you are unsure!
1291 Do not generate velocities. The velocities are set to zero
1292 when there are no velocities in the input structure file.
1296 Generate velocities in :ref:`gmx grompp` according to a
1297 Maxwell distribution at temperature :mdp:`gen-temp`, with
1298 random seed :mdp:`gen-seed`. This is only meaningful with
1299 :mdp-value:`integrator=md`.
1304 temperature for Maxwell distribution
1309 used to initialize random generator for random velocities,
1310 when :mdp:`gen-seed` is set to -1, a pseudo random seed is
1317 .. mdp:: constraints
1319 Controls which bonds in the topology will be converted to rigid
1320 holonomic constraints. Note that typical rigid water models do not
1321 have bonds, but rather a specialized ``[settles]`` directive, so
1322 are not affected by this keyword.
1326 No bonds converted to constraints.
1328 .. mdp-value:: h-bonds
1330 Convert the bonds with H-atoms to constraints.
1332 .. mdp-value:: all-bonds
1334 Convert all bonds to constraints.
1336 .. mdp-value:: h-angles
1338 Convert all bonds to constraints and convert the angles that
1339 involve H-atoms to bond-constraints.
1341 .. mdp-value:: all-angles
1343 Convert all bonds to constraints and all angles to bond-constraints.
1345 .. mdp:: constraint-algorithm
1347 Chooses which solver satisfies any non-SETTLE holonomic
1350 .. mdp-value:: LINCS
1352 LINear Constraint Solver. With domain decomposition the parallel
1353 version P-LINCS is used. The accuracy in set with
1354 :mdp:`lincs-order`, which sets the number of matrices in the
1355 expansion for the matrix inversion. After the matrix inversion
1356 correction the algorithm does an iterative correction to
1357 compensate for lengthening due to rotation. The number of such
1358 iterations can be controlled with :mdp:`lincs-iter`. The root
1359 mean square relative constraint deviation is printed to the log
1360 file every :mdp:`nstlog` steps. If a bond rotates more than
1361 :mdp:`lincs-warnangle` in one step, a warning will be printed
1362 both to the log file and to ``stderr``. LINCS should not be used
1363 with coupled angle constraints.
1365 .. mdp-value:: SHAKE
1367 SHAKE is slightly slower and less stable than LINCS, but does
1368 work with angle constraints. The relative tolerance is set with
1369 :mdp:`shake-tol`, 0.0001 is a good value for "normal" MD. SHAKE
1370 does not support constraints between atoms on different
1371 decomposition domains, so it can only be used with domain
1372 decomposition when so-called update-groups are used, which is
1373 usally the case when only bonds involving hydrogens are
1374 constrained. SHAKE can not be used with energy minimization.
1376 .. mdp:: continuation
1378 This option was formerly known as ``unconstrained-start``.
1382 apply constraints to the start configuration and reset shells
1386 do not apply constraints to the start configuration and do not
1387 reset shells, useful for exact coninuation and reruns
1392 relative tolerance for SHAKE
1394 .. mdp:: lincs-order
1397 Highest order in the expansion of the constraint coupling
1398 matrix. When constraints form triangles, an additional expansion of
1399 the same order is applied on top of the normal expansion only for
1400 the couplings within such triangles. For "normal" MD simulations an
1401 order of 4 usually suffices, 6 is needed for large time-steps with
1402 virtual sites or BD. For accurate energy minimization an order of 8
1403 or more might be required. With domain decomposition, the cell size
1404 is limited by the distance spanned by :mdp:`lincs-order` +1
1405 constraints. When one wants to scale further than this limit, one
1406 can decrease :mdp:`lincs-order` and increase :mdp:`lincs-iter`,
1407 since the accuracy does not deteriorate when (1+ :mdp:`lincs-iter`
1408 )* :mdp:`lincs-order` remains constant.
1413 Number of iterations to correct for rotational lengthening in
1414 LINCS. For normal runs a single step is sufficient, but for NVE
1415 runs where you want to conserve energy accurately or for accurate
1416 energy minimization you might want to increase it to 2.
1418 .. mdp:: lincs-warnangle
1421 maximum angle that a bond can rotate before LINCS will complain
1427 bonds are represented by a harmonic potential
1431 bonds are represented by a Morse potential
1434 Energy group exclusions
1435 ^^^^^^^^^^^^^^^^^^^^^^^
1437 .. mdp:: energygrp-excl
1439 Pairs of energy groups for which all non-bonded interactions are
1440 excluded. An example: if you have two energy groups ``Protein`` and
1441 ``SOL``, specifying ``energygrp-excl = Protein Protein SOL SOL``
1442 would give only the non-bonded interactions between the protein and
1443 the solvent. This is especially useful for speeding up energy
1444 calculations with ``mdrun -rerun`` and for excluding interactions
1445 within frozen groups.
1454 When set to 1 there is a wall at ``z=0``, when set to 2 there is
1455 also a wall at ``z=z-box``. Walls can only be used with :mdp:`pbc`
1456 ``=xy``. When set to 2, pressure coupling and Ewald summation can be
1457 used (it is usually best to use semiisotropic pressure coupling
1458 with the ``x/y`` compressibility set to 0, as otherwise the surface
1459 area will change). Walls interact wit the rest of the system
1460 through an optional :mdp:`wall-atomtype`. Energy groups ``wall0``
1461 and ``wall1`` (for :mdp:`nwall` =2) are added automatically to
1462 monitor the interaction of energy groups with each wall. The center
1463 of mass motion removal will be turned off in the ``z``-direction.
1465 .. mdp:: wall-atomtype
1467 the atom type name in the force field for each wall. By (for
1468 example) defining a special wall atom type in the topology with its
1469 own combination rules, this allows for independent tuning of the
1470 interaction of each atomtype with the walls.
1476 LJ integrated over the volume behind the wall: 9-3 potential
1480 LJ integrated over the wall surface: 10-4 potential
1484 direct LJ potential with the ``z`` distance from the wall
1488 user defined potentials indexed with the ``z`` distance from the
1489 wall, the tables are read analogously to the
1490 :mdp:`energygrp-table` option, where the first name is for a
1491 "normal" energy group and the second name is ``wall0`` or
1492 ``wall1``, only the dispersion and repulsion columns are used
1494 .. mdp:: wall-r-linpot
1497 Below this distance from the wall the potential is continued
1498 linearly and thus the force is constant. Setting this option to a
1499 postive value is especially useful for equilibration when some
1500 atoms are beyond a wall. When the value is <=0 (<0 for
1501 :mdp:`wall-type` =table), a fatal error is generated when atoms
1504 .. mdp:: wall-density
1506 [nm\ :sup:`-3`] / [nm\ :sup:`-2`]
1507 the number density of the atoms for each wall for wall types 9-3
1510 .. mdp:: wall-ewald-zfac
1513 The scaling factor for the third box vector for Ewald summation
1514 only, the minimum is 2. Ewald summation can only be used with
1515 :mdp:`nwall` =2, where one should use :mdp:`ewald-geometry`
1516 ``=3dc``. The empty layer in the box serves to decrease the
1517 unphysical Coulomb interaction between periodic images.
1523 Note that where pulling coordinates are applicable, there can be more
1524 than one (set with :mdp:`pull-ncoords`) and multiple related :ref:`mdp`
1525 variables will exist accordingly. Documentation references to things
1526 like :mdp:`pull-coord1-vec` should be understood to apply to to the
1527 applicable pulling coordinate, eg. the second pull coordinate is described by
1528 pull-coord2-vec, pull-coord2-k, and so on.
1534 No center of mass pulling. All the following pull options will
1535 be ignored (and if present in the :ref:`mdp` file, they unfortunately
1540 Center of mass pulling will be applied on 1 or more groups using
1541 1 or more pull coordinates.
1543 .. mdp:: pull-cylinder-r
1546 the radius of the cylinder for :mdp-value:`pull-coord1-geometry=cylinder`
1548 .. mdp:: pull-constr-tol
1551 the relative constraint tolerance for constraint pulling
1553 .. mdp:: pull-print-com
1557 do not print the COM for any group
1561 print the COM of all groups for all pull coordinates
1563 .. mdp:: pull-print-ref-value
1567 do not print the reference value for each pull coordinate
1571 print the reference value for each pull coordinate
1573 .. mdp:: pull-print-components
1577 only print the distance for each pull coordinate
1581 print the distance and Cartesian components selected in
1582 :mdp:`pull-coord1-dim`
1584 .. mdp:: pull-nstxout
1587 frequency for writing out the COMs of all the pull group (0 is
1590 .. mdp:: pull-nstfout
1593 frequency for writing out the force of all the pulled group
1596 .. mdp:: pull-pbc-ref-prev-step-com
1600 Use the reference atom (:mdp:`pull-group1-pbcatom`) for the
1601 treatment of periodic boundary conditions.
1605 Use the COM of the previous step as reference for the treatment
1606 of periodic boundary conditions. The reference is initialized
1607 using the reference atom (:mdp:`pull-group1-pbcatom`), which should
1608 be located centrally in the group. Using the COM from the
1609 previous step can be useful if one or more pull groups are large.
1611 .. mdp:: pull-xout-average
1615 Write the instantaneous coordinates for all the pulled groups.
1619 Write the average coordinates (since last output) for all the
1620 pulled groups. N.b., some analysis tools might expect instantaneous
1623 .. mdp:: pull-fout-average
1627 Write the instantaneous force for all the pulled groups.
1631 Write the average force (since last output) for all the
1632 pulled groups. N.b., some analysis tools might expect instantaneous
1635 .. mdp:: pull-ngroups
1638 The number of pull groups, not including the absolute reference
1639 group, when used. Pull groups can be reused in multiple pull
1640 coordinates. Below only the pull options for group 1 are given,
1641 further groups simply increase the group index number.
1643 .. mdp:: pull-ncoords
1646 The number of pull coordinates. Below only the pull options for
1647 coordinate 1 are given, further coordinates simply increase the
1648 coordinate index number.
1650 .. mdp:: pull-group1-name
1652 The name of the pull group, is looked up in the index file or in
1653 the default groups to obtain the atoms involved.
1655 .. mdp:: pull-group1-weights
1657 Optional relative weights which are multiplied with the masses of
1658 the atoms to give the total weight for the COM. The number should
1659 be 0, meaning all 1, or the number of atoms in the pull group.
1661 .. mdp:: pull-group1-pbcatom
1664 The reference atom for the treatment of periodic boundary
1665 conditions inside the group (this has no effect on the treatment of
1666 the pbc between groups). This option is only important when the
1667 diameter of the pull group is larger than half the shortest box
1668 vector. For determining the COM, all atoms in the group are put at
1669 their periodic image which is closest to
1670 :mdp:`pull-group1-pbcatom`. A value of 0 means that the middle
1671 atom (number wise) is used, which is only safe for small groups.
1672 :ref:`gmx grompp` checks that the maximum distance from the reference
1673 atom (specifically chosen, or not) to the other atoms in the group
1674 is not too large. This parameter is not used with
1675 :mdp:`pull-coord1-geometry` cylinder. A value of -1 turns on cosine
1676 weighting, which is useful for a group of molecules in a periodic
1677 system, *e.g.* a water slab (see Engin et al. J. Chem. Phys. B
1680 .. mdp:: pull-coord1-type
1682 .. mdp-value:: umbrella
1684 Center of mass pulling using an umbrella potential between the
1685 reference group and one or more groups.
1687 .. mdp-value:: constraint
1689 Center of mass pulling using a constraint between the reference
1690 group and one or more groups. The setup is identical to the
1691 option umbrella, except for the fact that a rigid constraint is
1692 applied instead of a harmonic potential. Note that this type is
1693 not supported in combination with multiple time stepping.
1695 .. mdp-value:: constant-force
1697 Center of mass pulling using a linear potential and therefore a
1698 constant force. For this option there is no reference position
1699 and therefore the parameters :mdp:`pull-coord1-init` and
1700 :mdp:`pull-coord1-rate` are not used.
1702 .. mdp-value:: flat-bottom
1704 At distances above :mdp:`pull-coord1-init` a harmonic potential
1705 is applied, otherwise no potential is applied.
1707 .. mdp-value:: flat-bottom-high
1709 At distances below :mdp:`pull-coord1-init` a harmonic potential
1710 is applied, otherwise no potential is applied.
1712 .. mdp-value:: external-potential
1714 An external potential that needs to be provided by another
1717 .. mdp:: pull-coord1-potential-provider
1719 The name of the external module that provides the potential for
1720 the case where :mdp:`pull-coord1-type` is external-potential.
1722 .. mdp:: pull-coord1-geometry
1724 .. mdp-value:: distance
1726 Pull along the vector connecting the two groups. Components can
1727 be selected with :mdp:`pull-coord1-dim`.
1729 .. mdp-value:: direction
1731 Pull in the direction of :mdp:`pull-coord1-vec`.
1733 .. mdp-value:: direction-periodic
1735 As :mdp-value:`pull-coord1-geometry=direction`, but does not apply
1736 periodic box vector corrections to keep the distance within half
1737 the box length. This is (only) useful for pushing groups apart
1738 by more than half the box length by continuously changing the reference
1739 location using a pull rate. With this geometry the box should not be
1740 dynamic (*e.g.* no pressure scaling) in the pull dimensions and
1741 the pull force is not added to the virial.
1743 .. mdp-value:: direction-relative
1745 As :mdp-value:`pull-coord1-geometry=direction`, but the pull vector is the vector
1746 that points from the COM of a third to the COM of a fourth pull
1747 group. This means that 4 groups need to be supplied in
1748 :mdp:`pull-coord1-groups`. Note that the pull force will give
1749 rise to a torque on the pull vector, which is turn leads to
1750 forces perpendicular to the pull vector on the two groups
1751 defining the vector. If you want a pull group to move between
1752 the two groups defining the vector, simply use the union of
1753 these two groups as the reference group.
1755 .. mdp-value:: cylinder
1757 Designed for pulling with respect to a layer where the reference
1758 COM is given by a local cylindrical part of the reference group.
1759 The pulling is in the direction of :mdp:`pull-coord1-vec`. From
1760 the first of the two groups in :mdp:`pull-coord1-groups` a
1761 cylinder is selected around the axis going through the COM of
1762 the second group with direction :mdp:`pull-coord1-vec` with
1763 radius :mdp:`pull-cylinder-r`. Weights of the atoms decrease
1764 continously to zero as the radial distance goes from 0 to
1765 :mdp:`pull-cylinder-r` (mass weighting is also used). The radial
1766 dependence gives rise to radial forces on both pull groups.
1767 Note that the radius should be smaller than half the box size.
1768 For tilted cylinders they should be even smaller than half the
1769 box size since the distance of an atom in the reference group
1770 from the COM of the pull group has both a radial and an axial
1771 component. This geometry is not supported with constraint
1774 .. mdp-value:: angle
1776 Pull along an angle defined by four groups. The angle is
1777 defined as the angle between two vectors: the vector connecting
1778 the COM of the first group to the COM of the second group and
1779 the vector connecting the COM of the third group to the COM of
1782 .. mdp-value:: angle-axis
1784 As :mdp-value:`pull-coord1-geometry=angle` but the second vector is given by :mdp:`pull-coord1-vec`.
1785 Thus, only the two groups that define the first vector need to be given.
1787 .. mdp-value:: dihedral
1789 Pull along a dihedral angle defined by six groups. These pairwise
1790 define three vectors: the vector connecting the COM of group 1
1791 to the COM of group 2, the COM of group 3 to the COM of group 4,
1792 and the COM of group 5 to the COM group 6. The dihedral angle is
1793 then defined as the angle between two planes: the plane spanned by the
1794 the two first vectors and the plane spanned the two last vectors.
1797 .. mdp:: pull-coord1-groups
1799 The group indices on which this pull coordinate will operate.
1800 The number of group indices required is geometry dependent.
1801 The first index can be 0, in which case an
1802 absolute reference of :mdp:`pull-coord1-origin` is used. With an
1803 absolute reference the system is no longer translation invariant
1804 and one should think about what to do with the center of mass
1807 .. mdp:: pull-coord1-dim
1810 Selects the dimensions that this pull coordinate acts on and that
1811 are printed to the output files when
1812 :mdp:`pull-print-components` = :mdp-value:`pull-coord1-start=yes`. With
1813 :mdp:`pull-coord1-geometry` = :mdp-value:`pull-coord1-geometry=distance`, only Cartesian
1814 components set to Y contribute to the distance. Thus setting this
1815 to Y Y N results in a distance in the x/y plane. With other
1816 geometries all dimensions with non-zero entries in
1817 :mdp:`pull-coord1-vec` should be set to Y, the values for other
1818 dimensions only affect the output.
1820 .. mdp:: pull-coord1-origin
1823 The pull reference position for use with an absolute reference.
1825 .. mdp:: pull-coord1-vec
1828 The pull direction. :ref:`gmx grompp` normalizes the vector.
1830 .. mdp:: pull-coord1-start
1834 do not modify :mdp:`pull-coord1-init`
1838 add the COM distance of the starting conformation to
1839 :mdp:`pull-coord1-init`
1841 .. mdp:: pull-coord1-init
1844 The reference distance or reference angle at t=0.
1846 .. mdp:: pull-coord1-rate
1848 (0) [nm/ps] or [deg/ps]
1849 The rate of change of the reference position or reference angle.
1851 .. mdp:: pull-coord1-k
1853 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`] or
1854 [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`]
1855 The force constant. For umbrella pulling this is the harmonic force
1856 constant in kJ mol\ :sup:`-1` nm\ :sup:`-2` (or kJ mol\ :sup:`-1` rad\ :sup:`-2`
1857 for angles). For constant force pulling this is the
1858 force constant of the linear potential, and thus the negative (!)
1859 of the constant force in kJ mol\ :sup:`-1` nm\ :sup:`-1`
1860 (or kJ mol\ :sup:`-1` rad\ :sup:`-1` for angles).
1861 Note that for angles the force constant is expressed in terms of radians
1862 (while :mdp:`pull-coord1-init` and :mdp:`pull-coord1-rate` are expressed in degrees).
1864 .. mdp:: pull-coord1-kB
1866 (pull-k1) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`]
1867 or [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`]
1868 As :mdp:`pull-coord1-k`, but for state B. This is only used when
1869 :mdp:`free-energy` is turned on. The force constant is then (1 -
1870 lambda) * :mdp:`pull-coord1-k` + lambda * :mdp:`pull-coord1-kB`.
1872 AWH adaptive biasing
1873 ^^^^^^^^^^^^^^^^^^^^
1883 Adaptively bias a reaction coordinate using the AWH method and estimate
1884 the corresponding PMF. The PMF and other AWH data are written to energy
1885 file at an interval set by :mdp:`awh-nstout` and can be extracted with
1886 the ``gmx awh`` tool. The AWH coordinate can be
1887 multidimensional and is defined by mapping each dimension to a pull coordinate index.
1888 This is only allowed if :mdp-value:`pull-coord1-type=external-potential` and
1889 :mdp:`pull-coord1-potential-provider` = ``awh`` for the concerned pull coordinate
1890 indices. Pull geometry 'direction-periodic' is not supported by AWH.
1892 .. mdp:: awh-potential
1894 .. mdp-value:: convolved
1896 The applied biasing potential is the convolution of the bias function and a
1897 set of harmonic umbrella potentials (see :mdp-value:`awh-potential=umbrella` below). This results
1898 in a smooth potential function and force. The resolution of the potential is set
1899 by the force constant of each umbrella, see :mdp:`awh1-dim1-force-constant`.
1901 .. mdp-value:: umbrella
1903 The potential bias is applied by controlling the position of an harmonic potential
1904 using Monte-Carlo sampling. The force constant is set with
1905 :mdp:`awh1-dim1-force-constant`. The umbrella location
1906 is sampled using Monte-Carlo every :mdp:`awh-nstsample` steps.
1907 There are no advantages to using an umbrella.
1908 This option is mainly for comparison and testing purposes.
1910 .. mdp:: awh-share-multisim
1914 AWH will not share biases across simulations started with
1915 :ref:`gmx mdrun` option ``-multidir``. The biases will be independent.
1919 With :ref:`gmx mdrun` and option ``-multidir`` the bias and PMF estimates
1920 for biases with :mdp:`awh1-share-group` >0 will be shared across simulations
1921 with the biases with the same :mdp:`awh1-share-group` value.
1922 The simulations should have the same AWH settings for sharing to make sense.
1923 :ref:`gmx mdrun` will check whether the simulations are technically
1924 compatible for sharing, but the user should check that bias sharing
1925 physically makes sense.
1929 (-1) Random seed for Monte-Carlo sampling the umbrella position,
1930 where -1 indicates to generate a seed. Only used with
1931 :mdp-value:`awh-potential=umbrella`.
1936 Number of steps between printing AWH data to the energy file, should be
1937 a multiple of :mdp:`nstenergy`.
1939 .. mdp:: awh-nstsample
1942 Number of steps between sampling of the coordinate value. This sampling
1943 is the basis for updating the bias and estimating the PMF and other AWH observables.
1945 .. mdp:: awh-nsamples-update
1948 The number of coordinate samples used for each AWH update.
1949 The update interval in steps is :mdp:`awh-nstsample` times this value.
1954 The number of biases, each acting on its own coordinate.
1955 The following options should be specified
1956 for each bias although below only the options for bias number 1 is shown. Options for
1957 other bias indices are obtained by replacing '1' by the bias index.
1959 .. mdp:: awh1-error-init
1961 (10.0) [kJ mol\ :sup:`-1`]
1962 Estimated initial average error of the PMF for this bias. This value together with the
1963 given diffusion constant(s) :mdp:`awh1-dim1-diffusion` determine the initial biasing rate.
1964 The error is obviously not known *a priori*. Only a rough estimate of :mdp:`awh1-error-init`
1966 As a general guideline, leave :mdp:`awh1-error-init` to its default value when starting a new
1967 simulation. On the other hand, when there is *a priori* knowledge of the PMF (e.g. when
1968 an initial PMF estimate is provided, see the :mdp:`awh1-user-data` option)
1969 then :mdp:`awh1-error-init` should reflect that knowledge.
1971 .. mdp:: awh1-growth
1973 .. mdp-value:: exp-linear
1975 Each bias keeps a reference weight histogram for the coordinate samples.
1976 Its size sets the magnitude of the bias function and free energy estimate updates
1977 (few samples corresponds to large updates and vice versa).
1978 Thus, its growth rate sets the maximum convergence rate.
1979 By default, there is an initial stage in which the histogram grows close to exponentially (but slower than the sampling rate).
1980 In the final stage that follows, the growth rate is linear and equal to the sampling rate (set by :mdp:`awh-nstsample`).
1981 The initial stage is typically necessary for efficient convergence when starting a new simulation where
1982 high free energy barriers have not yet been flattened by the bias.
1984 .. mdp-value:: linear
1986 As :mdp-value:`awh1-growth=exp-linear` but skip the initial stage. This may be useful if there is *a priori*
1987 knowledge (see :mdp:`awh1-error-init`) which eliminates the need for an initial stage. This is also
1988 the setting compatible with :mdp-value:`awh1-target=local-boltzmann`.
1990 .. mdp:: awh1-equilibrate-histogram
1994 Do not equilibrate histogram.
1998 Before entering the initial stage (see :mdp-value:`awh1-growth=exp-linear`), make sure the
1999 histogram of sampled weights is following the target distribution closely enough (specifically,
2000 at least 80% of the target region needs to have a local relative error of less than 20%). This
2001 option would typically only be used when :mdp:`awh1-share-group` > 0
2002 and the initial configurations poorly represent the target
2005 .. mdp:: awh1-target
2007 .. mdp-value:: constant
2009 The bias is tuned towards a constant (uniform) coordinate distribution
2010 in the defined sampling interval (defined by [:mdp:`awh1-dim1-start`, :mdp:`awh1-dim1-end`]).
2012 .. mdp-value:: cutoff
2014 Similar to :mdp-value:`awh1-target=constant`, but the target
2015 distribution is proportional to 1/(1 + exp(F - :mdp-value:`awh1-target=cutoff`)),
2016 where F is the free energy relative to the estimated global minimum.
2017 This provides a smooth switch of a flat target distribution in
2018 regions with free energy lower than the cut-off to a Boltzmann
2019 distribution in regions with free energy higher than the cut-off.
2021 .. mdp-value:: boltzmann
2023 The target distribution is a Boltzmann distribtution with a scaled beta (inverse temperature)
2024 factor given by :mdp:`awh1-target-beta-scaling`. *E.g.*, a value of 0.1
2025 would give the same coordinate distribution as sampling with a simulation temperature
2028 .. mdp-value:: local-boltzmann
2030 Same target distribution and use of :mdp:`awh1-target-beta-scaling`
2031 but the convergence towards the target distribution is inherently local *i.e.*, the rate of
2032 change of the bias only depends on the local sampling. This local convergence property is
2033 only compatible with :mdp-value:`awh1-growth=linear`, since for
2034 :mdp-value:`awh1-growth=exp-linear` histograms are globally rescaled in the initial stage.
2036 .. mdp:: awh1-target-beta-scaling
2039 For :mdp-value:`awh1-target=boltzmann` and :mdp-value:`awh1-target=local-boltzmann`
2040 it is the unitless beta scaling factor taking values in (0,1).
2042 .. mdp:: awh1-target-cutoff
2044 (0) [kJ mol\ :sup:`-1`]
2045 For :mdp-value:`awh1-target=cutoff` this is the cutoff, should be > 0.
2047 .. mdp:: awh1-user-data
2051 Initialize the PMF and target distribution with default values.
2055 Initialize the PMF and target distribution with user provided data. For :mdp:`awh-nbias` = 1,
2056 :ref:`gmx mdrun` will expect a file ``awhinit.xvg`` to be present in the run directory.
2057 For multiple biases, :ref:`gmx mdrun` expects files ``awhinit1.xvg``, ``awhinit2.xvg``, etc.
2058 The file name can be changed with the ``-awh`` option.
2059 The first :mdp:`awh1-ndim` columns of
2060 each input file should contain the coordinate values, such that each row defines a point in
2061 coordinate space. Column :mdp:`awh1-ndim` + 1 should contain the PMF value (in kT) for each point.
2062 The target distribution column can either follow the PMF (column :mdp:`awh1-ndim` + 2) or
2063 be in the same column as written by :ref:`gmx awh`.
2065 .. mdp:: awh1-share-group
2069 Do not share the bias.
2071 .. mdp-value:: positive
2073 Share the bias and PMF estimates within and/or between simulations.
2074 Within a simulation, the bias will be shared between biases that have the
2075 same :mdp:`awh1-share-group` index (note that the current code does not support this).
2076 With :mdp-value:`awh-share-multisim=yes` and
2077 :ref:`gmx mdrun` option ``-multidir`` the bias will also be shared across simulations.
2078 Sharing may increase convergence initially, although the starting configurations
2079 can be critical, especially when sharing between many biases.
2080 Currently, positive group values should start at 1 and increase
2081 by 1 for each subsequent bias that is shared.
2086 Number of dimensions of the coordinate, each dimension maps to 1 pull coordinate.
2087 The following options should be specified for each such dimension. Below only
2088 the options for dimension number 1 is shown. Options for other dimension indices are
2089 obtained by replacing '1' by the dimension index.
2091 .. mdp:: awh1-dim1-coord-provider
2095 The pull module is providing the reaction coordinate for this dimension.
2096 With multiple time-stepping, AWH and pull should be in the same MTS level.
2098 .. mdp-value:: fep-lambda
2100 The free energy lambda state is the reaction coordinate for this dimension.
2101 The lambda states to use are specified by :mdp:`fep-lambdas`, :mdp:`vdw-lambdas`,
2102 :mdp:`coul-lambdas` etc. This is not compatible with delta-lambda. It also requires
2103 calc-lambda-neighbors to be -1. With multiple time-stepping, AWH should
2104 be in the slow level.
2106 .. mdp:: awh1-dim1-coord-index
2109 Index of the pull coordinate defining this coordinate dimension.
2111 .. mdp:: awh1-dim1-force-constant
2113 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-2`]
2114 Force constant for the (convolved) umbrella potential(s) along this
2115 coordinate dimension.
2117 .. mdp:: awh1-dim1-start
2120 Start value of the sampling interval along this dimension. The range of allowed
2121 values depends on the relevant pull geometry (see :mdp:`pull-coord1-geometry`).
2122 For dihedral geometries :mdp:`awh1-dim1-start` greater than :mdp:`awh1-dim1-end`
2123 is allowed. The interval will then wrap around from +period/2 to -period/2.
2124 For the direction geometry, the dimension is made periodic when
2125 the direction is along a box vector and covers more than 95%
2126 of the box length. Note that one should not apply pressure coupling
2127 along a periodic dimension.
2129 .. mdp:: awh1-dim1-end
2132 End value defining the sampling interval together with :mdp:`awh1-dim1-start`.
2134 .. mdp:: awh1-dim1-diffusion
2136 (10\ :sup:`-5`) [nm\ :sup:`2`/ps], [rad\ :sup:`2`/ps] or [ps\ :sup:`-1`]
2137 Estimated diffusion constant for this coordinate dimension determining the initial
2138 biasing rate. This needs only be a rough estimate and should not critically
2139 affect the results unless it is set to something very low, leading to slow convergence,
2140 or very high, forcing the system far from equilibrium. Not setting this value
2141 explicitly generates a warning.
2143 .. mdp:: awh1-dim1-cover-diameter
2146 Diameter that needs to be sampled by a single simulation around a coordinate value
2147 before the point is considered covered in the initial stage (see :mdp-value:`awh1-growth=exp-linear`).
2148 A value > 0 ensures that for each covering there is a continuous transition of this diameter
2149 across each coordinate value.
2150 This is trivially true for independent simulations but not for for multiple bias-sharing simulations
2151 (:mdp:`awh1-share-group`>0).
2152 For a diameter = 0, covering occurs as soon as the simulations have sampled the whole interval, which
2153 for many sharing simulations does not guarantee transitions across free energy barriers.
2154 On the other hand, when the diameter >= the sampling interval length, covering occurs when a single simulation
2155 has independently sampled the whole interval.
2160 These :ref:`mdp` parameters can be used enforce the rotation of a group of atoms,
2161 e.g. a protein subunit. The `reference manual`_ describes in detail 13 different potentials
2162 that can be used to achieve such a rotation.
2168 No enforced rotation will be applied. All enforced rotation options will
2169 be ignored (and if present in the :ref:`mdp` file, they unfortunately
2174 Apply the rotation potential specified by :mdp:`rot-type0` to the group of atoms given
2175 under the :mdp:`rot-group0` option.
2177 .. mdp:: rot-ngroups
2180 Number of rotation groups.
2184 Name of rotation group 0 in the index file.
2189 Type of rotation potential that is applied to rotation group 0. Can be of of the following:
2190 ``iso``, ``iso-pf``, ``pm``, ``pm-pf``, ``rm``, ``rm-pf``, ``rm2``, ``rm2-pf``,
2191 ``flex``, ``flex-t``, ``flex2``, or ``flex2-t``.
2196 Use mass weighted rotation group positions.
2201 Rotation vector, will get normalized.
2206 Pivot point for the potentials ``iso``, ``pm``, ``rm``, and ``rm2``.
2210 (0) [degree ps\ :sup:`-1`]
2211 Reference rotation rate of group 0.
2215 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
2216 Force constant for group 0.
2218 .. mdp:: rot-slab-dist0
2221 Slab distance, if a flexible axis rotation type was chosen.
2223 .. mdp:: rot-min-gauss0
2226 Minimum value (cutoff) of Gaussian function for the force to be evaluated
2227 (for the flexible axis potentials).
2231 (0.0001) [nm\ :sup:`2`]
2232 Value of additive constant epsilon for ``rm2*`` and ``flex2*`` potentials.
2234 .. mdp:: rot-fit-method0
2237 Fitting method when determining the actual angle of a rotation group
2238 (can be one of ``rmsd``, ``norm``, or ``potential``).
2240 .. mdp:: rot-potfit-nsteps0
2243 For fit type ``potential``, the number of angular positions around the reference angle for which the
2244 rotation potential is evaluated.
2246 .. mdp:: rot-potfit-step0
2249 For fit type ``potential``, the distance in degrees between two angular positions.
2251 .. mdp:: rot-nstrout
2254 Output frequency (in steps) for the angle of the rotation group, as well as for the torque
2255 and the rotation potential energy.
2257 .. mdp:: rot-nstsout
2260 Output frequency for per-slab data of the flexible axis potentials, i.e. angles, torques and slab centers.
2270 ignore distance restraint information in topology file
2272 .. mdp-value:: simple
2274 simple (per-molecule) distance restraints.
2276 .. mdp-value:: ensemble
2278 distance restraints over an ensemble of molecules in one
2279 simulation box. Normally, one would perform ensemble averaging
2280 over multiple simulations, using ``mdrun
2281 -multidir``. The environment
2282 variable ``GMX_DISRE_ENSEMBLE_SIZE`` sets the number of systems
2283 within each ensemble (usually equal to the number of directories
2284 supplied to ``mdrun -multidir``).
2286 .. mdp:: disre-weighting
2288 .. mdp-value:: equal
2290 divide the restraint force equally over all atom pairs in the
2293 .. mdp-value:: conservative
2295 the forces are the derivative of the restraint potential, this
2296 results in an weighting of the atom pairs to the reciprocal
2297 seventh power of the displacement. The forces are conservative
2298 when :mdp:`disre-tau` is zero.
2300 .. mdp:: disre-mixed
2304 the violation used in the calculation of the restraint force is
2305 the time-averaged violation
2309 the violation used in the calculation of the restraint force is
2310 the square root of the product of the time-averaged violation
2311 and the instantaneous violation
2315 (1000) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
2316 force constant for distance restraints, which is multiplied by a
2317 (possibly) different factor for each restraint given in the ``fac``
2318 column of the interaction in the topology file.
2323 time constant for distance restraints running average. A value of
2324 zero turns off time averaging.
2326 .. mdp:: nstdisreout
2329 period between steps when the running time-averaged and
2330 instantaneous distances of all atom pairs involved in restraints
2331 are written to the energy file (can make the energy file very
2338 ignore orientation restraint information in topology file
2342 use orientation restraints, ensemble averaging can be performed
2343 with ``mdrun -multidir``
2347 (0) [kJ mol\ :sup:`-1`]
2348 force constant for orientation restraints, which is multiplied by a
2349 (possibly) different weight factor for each restraint, can be set
2350 to zero to obtain the orientations from a free simulation
2355 time constant for orientation restraints running average. A value
2356 of zero turns off time averaging.
2358 .. mdp:: orire-fitgrp
2360 fit group for orientation restraining. This group of atoms is used
2361 to determine the rotation **R** of the system with respect to the
2362 reference orientation. The reference orientation is the starting
2363 conformation of the first subsystem. For a protein, backbone is a
2366 .. mdp:: nstorireout
2369 period between steps when the running time-averaged and
2370 instantaneous orientations for all restraints, and the molecular
2371 order tensor are written to the energy file (can make the energy
2375 Free energy calculations
2376 ^^^^^^^^^^^^^^^^^^^^^^^^
2378 .. mdp:: free-energy
2382 Only use topology A.
2386 Interpolate between topology A (lambda=0) to topology B
2387 (lambda=1) and write the derivative of the Hamiltonian with
2388 respect to lambda (as specified with :mdp:`dhdl-derivatives`),
2389 or the Hamiltonian differences with respect to other lambda
2390 values (as specified with foreign lambda) to the energy file
2391 and/or to ``dhdl.xvg``, where they can be processed by, for
2392 example :ref:`gmx bar`. The potentials, bond-lengths and angles
2393 are interpolated linearly as described in the manual. When
2394 :mdp:`sc-alpha` is larger than zero, soft-core potentials are
2395 used for the LJ and Coulomb interactions.
2399 Turns on expanded ensemble simulation, where the alchemical state
2400 becomes a dynamic variable, allowing jumping between different
2401 Hamiltonians. See the expanded ensemble options for controlling how
2402 expanded ensemble simulations are performed. The different
2403 Hamiltonians used in expanded ensemble simulations are defined by
2404 the other free energy options.
2406 .. mdp:: init-lambda
2409 starting value for lambda (float). Generally, this should only be
2410 used with slow growth (*i.e.* nonzero :mdp:`delta-lambda`). In
2411 other cases, :mdp:`init-lambda-state` should be specified
2412 instead. Must be greater than or equal to 0.
2414 .. mdp:: delta-lambda
2417 increment per time step for lambda
2419 .. mdp:: init-lambda-state
2422 starting value for the lambda state (integer). Specifies which
2423 columm of the lambda vector (:mdp:`coul-lambdas`,
2424 :mdp:`vdw-lambdas`, :mdp:`bonded-lambdas`,
2425 :mdp:`restraint-lambdas`, :mdp:`mass-lambdas`,
2426 :mdp:`temperature-lambdas`, :mdp:`fep-lambdas`) should be
2427 used. This is a zero-based index: :mdp:`init-lambda-state` 0 means
2428 the first column, and so on.
2430 .. mdp:: fep-lambdas
2433 Zero, one or more lambda values for which Delta H values will be
2434 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2435 steps. Values must be between 0 and 1. Free energy differences
2436 between different lambda values can then be determined with
2437 :ref:`gmx bar`. :mdp:`fep-lambdas` is different from the
2438 other -lambdas keywords because all components of the lambda vector
2439 that are not specified will use :mdp:`fep-lambdas` (including
2440 :mdp:`restraint-lambdas` and therefore the pull code restraints).
2442 .. mdp:: coul-lambdas
2445 Zero, one or more lambda values for which Delta H values will be
2446 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2447 steps. Values must be between 0 and 1. Only the electrostatic
2448 interactions are controlled with this component of the lambda
2449 vector (and only if the lambda=0 and lambda=1 states have differing
2450 electrostatic interactions).
2452 .. mdp:: vdw-lambdas
2455 Zero, one or more lambda values for which Delta H values will be
2456 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2457 steps. Values must be between 0 and 1. Only the van der Waals
2458 interactions are controlled with this component of the lambda
2461 .. mdp:: bonded-lambdas
2464 Zero, one or more lambda values for which Delta H values will be
2465 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2466 steps. Values must be between 0 and 1. Only the bonded interactions
2467 are controlled with this component of the lambda vector.
2469 .. mdp:: restraint-lambdas
2472 Zero, one or more lambda values for which Delta H values will be
2473 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2474 steps. Values must be between 0 and 1. Only the restraint
2475 interactions: dihedral restraints, and the pull code restraints are
2476 controlled with this component of the lambda vector.
2478 .. mdp:: mass-lambdas
2481 Zero, one or more lambda values for which Delta H values will be
2482 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2483 steps. Values must be between 0 and 1. Only the particle masses are
2484 controlled with this component of the lambda vector.
2486 .. mdp:: temperature-lambdas
2489 Zero, one or more lambda values for which Delta H values will be
2490 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2491 steps. Values must be between 0 and 1. Only the temperatures
2492 controlled with this component of the lambda vector. Note that
2493 these lambdas should not be used for replica exchange, only for
2494 simulated tempering.
2496 .. mdp:: calc-lambda-neighbors
2499 Controls the number of lambda values for which Delta H values will
2500 be calculated and written out, if :mdp:`init-lambda-state` has
2501 been set. A positive value will limit the number of lambda points
2502 calculated to only the nth neighbors of :mdp:`init-lambda-state`:
2503 for example, if :mdp:`init-lambda-state` is 5 and this parameter
2504 has a value of 2, energies for lambda points 3-7 will be calculated
2505 and writen out. A value of -1 means all lambda points will be
2506 written out. For normal BAR such as with :ref:`gmx bar`, a value of
2507 1 is sufficient, while for MBAR -1 should be used.
2512 the soft-core alpha parameter, a value of 0 results in linear
2513 interpolation of the LJ and Coulomb interactions
2518 power 6 for the radial term in the soft-core equation.
2523 Whether to apply the soft-core free energy interaction
2524 transformation to the Columbic interaction of a molecule. Default
2525 is no, as it is generally more efficient to turn off the Coulomic
2526 interactions linearly before turning off the van der Waals
2527 interactions. Note that it is only taken into account when lambda
2528 states are used, not with :mdp:`couple-lambda0` /
2529 :mdp:`couple-lambda1`, and you can still turn off soft-core
2530 interactions by setting :mdp:`sc-alpha` to 0.
2535 the power for lambda in the soft-core function, only the values 1
2541 the soft-core sigma for particles which have a C6 or C12 parameter
2542 equal to zero or a sigma smaller than :mdp:`sc-sigma`
2544 .. mdp:: couple-moltype
2546 Here one can supply a molecule type (as defined in the topology)
2547 for calculating solvation or coupling free energies. There is a
2548 special option ``system`` that couples all molecule types in the
2549 system. This can be useful for equilibrating a system starting from
2550 (nearly) random coordinates. :mdp:`free-energy` has to be turned
2551 on. The Van der Waals interactions and/or charges in this molecule
2552 type can be turned on or off between lambda=0 and lambda=1,
2553 depending on the settings of :mdp:`couple-lambda0` and
2554 :mdp:`couple-lambda1`. If you want to decouple one of several
2555 copies of a molecule, you need to copy and rename the molecule
2556 definition in the topology.
2558 .. mdp:: couple-lambda0
2560 .. mdp-value:: vdw-q
2562 all interactions are on at lambda=0
2566 the charges are zero (no Coulomb interactions) at lambda=0
2570 the Van der Waals interactions are turned at lambda=0; soft-core
2571 interactions will be required to avoid singularities
2575 the Van der Waals interactions are turned off and the charges
2576 are zero at lambda=0; soft-core interactions will be required to
2577 avoid singularities.
2579 .. mdp:: couple-lambda1
2581 analogous to :mdp:`couple-lambda1`, but for lambda=1
2583 .. mdp:: couple-intramol
2587 All intra-molecular non-bonded interactions for moleculetype
2588 :mdp:`couple-moltype` are replaced by exclusions and explicit
2589 pair interactions. In this manner the decoupled state of the
2590 molecule corresponds to the proper vacuum state without
2591 periodicity effects.
2595 The intra-molecular Van der Waals and Coulomb interactions are
2596 also turned on/off. This can be useful for partitioning
2597 free-energies of relatively large molecules, where the
2598 intra-molecular non-bonded interactions might lead to
2599 kinetically trapped vacuum conformations. The 1-4 pair
2600 interactions are not turned off.
2605 the frequency for writing dH/dlambda and possibly Delta H to
2606 dhdl.xvg, 0 means no ouput, should be a multiple of
2607 :mdp:`nstcalcenergy`.
2609 .. mdp:: dhdl-derivatives
2613 If yes (the default), the derivatives of the Hamiltonian with
2614 respect to lambda at each :mdp:`nstdhdl` step are written
2615 out. These values are needed for interpolation of linear energy
2616 differences with :ref:`gmx bar` (although the same can also be
2617 achieved with the right foreign lambda setting, that may not be as
2618 flexible), or with thermodynamic integration
2620 .. mdp:: dhdl-print-energy
2624 Include either the total or the potential energy in the dhdl
2625 file. Options are 'no', 'potential', or 'total'. This information
2626 is needed for later free energy analysis if the states of interest
2627 are at different temperatures. If all states are at the same
2628 temperature, this information is not needed. 'potential' is useful
2629 in case one is using ``mdrun -rerun`` to generate the ``dhdl.xvg``
2630 file. When rerunning from an existing trajectory, the kinetic
2631 energy will often not be correct, and thus one must compute the
2632 residual free energy from the potential alone, with the kinetic
2633 energy component computed analytically.
2635 .. mdp:: separate-dhdl-file
2639 The free energy values that are calculated (as specified with
2640 the foreign lambda and :mdp:`dhdl-derivatives` settings) are
2641 written out to a separate file, with the default name
2642 ``dhdl.xvg``. This file can be used directly with :ref:`gmx
2647 The free energy values are written out to the energy output file
2648 (``ener.edr``, in accumulated blocks at every :mdp:`nstenergy`
2649 steps), where they can be extracted with :ref:`gmx energy` or
2650 used directly with :ref:`gmx bar`.
2652 .. mdp:: dh-hist-size
2655 If nonzero, specifies the size of the histogram into which the
2656 Delta H values (specified with foreign lambda) and the derivative
2657 dH/dl values are binned, and written to ener.edr. This can be used
2658 to save disk space while calculating free energy differences. One
2659 histogram gets written for each foreign lambda and two for the
2660 dH/dl, at every :mdp:`nstenergy` step. Be aware that incorrect
2661 histogram settings (too small size or too wide bins) can introduce
2662 errors. Do not use histograms unless you're certain you need it.
2664 .. mdp:: dh-hist-spacing
2667 Specifies the bin width of the histograms, in energy units. Used in
2668 conjunction with :mdp:`dh-hist-size`. This size limits the
2669 accuracy with which free energies can be calculated. Do not use
2670 histograms unless you're certain you need it.
2673 Expanded Ensemble calculations
2674 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2676 .. mdp:: nstexpanded
2678 The number of integration steps beween attempted moves changing the
2679 system Hamiltonian in expanded ensemble simulations. Must be a
2680 multiple of :mdp:`nstcalcenergy`, but can be greater or less than
2687 No Monte Carlo in state space is performed.
2689 .. mdp-value:: metropolis-transition
2691 Uses the Metropolis weights to update the expanded ensemble
2692 weight of each state. Min{1,exp(-(beta_new u_new - beta_old
2695 .. mdp-value:: barker-transition
2697 Uses the Barker transition critera to update the expanded
2698 ensemble weight of each state i, defined by exp(-beta_new
2699 u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2701 .. mdp-value:: wang-landau
2703 Uses the Wang-Landau algorithm (in state space, not energy
2704 space) to update the expanded ensemble weights.
2706 .. mdp-value:: min-variance
2708 Uses the minimum variance updating method of Escobedo et al. to
2709 update the expanded ensemble weights. Weights will not be the
2710 free energies, but will rather emphasize states that need more
2711 sampling to give even uncertainty.
2713 .. mdp:: lmc-mc-move
2717 No Monte Carlo in state space is performed.
2719 .. mdp-value:: metropolis-transition
2721 Randomly chooses a new state up or down, then uses the
2722 Metropolis critera to decide whether to accept or reject:
2723 Min{1,exp(-(beta_new u_new - beta_old u_old)}
2725 .. mdp-value:: barker-transition
2727 Randomly chooses a new state up or down, then uses the Barker
2728 transition critera to decide whether to accept or reject:
2729 exp(-beta_new u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2731 .. mdp-value:: gibbs
2733 Uses the conditional weights of the state given the coordinate
2734 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2737 .. mdp-value:: metropolized-gibbs
2739 Uses the conditional weights of the state given the coordinate
2740 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2741 to move to, EXCLUDING the current state, then uses a rejection
2742 step to ensure detailed balance. Always more efficient that
2743 Gibbs, though only marginally so in many situations, such as
2744 when only the nearest neighbors have decent phase space
2750 random seed to use for Monte Carlo moves in state space. When
2751 :mdp:`lmc-seed` is set to -1, a pseudo random seed is us
2753 .. mdp:: mc-temperature
2755 Temperature used for acceptance/rejection for Monte Carlo moves. If
2756 not specified, the temperature of the simulation specified in the
2757 first group of :mdp:`ref-t` is used.
2762 The cutoff for the histogram of state occupancies to be reset, and
2763 the free energy incrementor to be changed from delta to delta *
2764 :mdp:`wl-scale`. If we define the Nratio = (number of samples at
2765 each histogram) / (average number of samples at each
2766 histogram). :mdp:`wl-ratio` of 0.8 means that means that the
2767 histogram is only considered flat if all Nratio > 0.8 AND
2768 simultaneously all 1/Nratio > 0.8.
2773 Each time the histogram is considered flat, then the current value
2774 of the Wang-Landau incrementor for the free energies is multiplied
2775 by :mdp:`wl-scale`. Value must be between 0 and 1.
2777 .. mdp:: init-wl-delta
2780 The initial value of the Wang-Landau incrementor in kT. Some value
2781 near 1 kT is usually most efficient, though sometimes a value of
2782 2-3 in units of kT works better if the free energy differences are
2785 .. mdp:: wl-oneovert
2788 Set Wang-Landau incrementor to scale with 1/(simulation time) in
2789 the large sample limit. There is significant evidence that the
2790 standard Wang-Landau algorithms in state space presented here
2791 result in free energies getting 'burned in' to incorrect values
2792 that depend on the initial state. when :mdp:`wl-oneovert` is true,
2793 then when the incrementor becomes less than 1/N, where N is the
2794 mumber of samples collected (and thus proportional to the data
2795 collection time, hence '1 over t'), then the Wang-Lambda
2796 incrementor is set to 1/N, decreasing every step. Once this occurs,
2797 :mdp:`wl-ratio` is ignored, but the weights will still stop
2798 updating when the equilibration criteria set in
2799 :mdp:`lmc-weights-equil` is achieved.
2801 .. mdp:: lmc-repeats
2804 Controls the number of times that each Monte Carlo swap type is
2805 performed each iteration. In the limit of large numbers of Monte
2806 Carlo repeats, then all methods converge to Gibbs sampling. The
2807 value will generally not need to be different from 1.
2809 .. mdp:: lmc-gibbsdelta
2812 Limit Gibbs sampling to selected numbers of neighboring states. For
2813 Gibbs sampling, it is sometimes inefficient to perform Gibbs
2814 sampling over all of the states that are defined. A positive value
2815 of :mdp:`lmc-gibbsdelta` means that only states plus or minus
2816 :mdp:`lmc-gibbsdelta` are considered in exchanges up and down. A
2817 value of -1 means that all states are considered. For less than 100
2818 states, it is probably not that expensive to include all states.
2820 .. mdp:: lmc-forced-nstart
2823 Force initial state space sampling to generate weights. In order to
2824 come up with reasonable initial weights, this setting allows the
2825 simulation to drive from the initial to the final lambda state,
2826 with :mdp:`lmc-forced-nstart` steps at each state before moving on
2827 to the next lambda state. If :mdp:`lmc-forced-nstart` is
2828 sufficiently long (thousands of steps, perhaps), then the weights
2829 will be close to correct. However, in most cases, it is probably
2830 better to simply run the standard weight equilibration algorithms.
2832 .. mdp:: nst-transition-matrix
2835 Frequency of outputting the expanded ensemble transition matrix. A
2836 negative number means it will only be printed at the end of the
2839 .. mdp:: symmetrized-transition-matrix
2842 Whether to symmetrize the empirical transition matrix. In the
2843 infinite limit the matrix will be symmetric, but will diverge with
2844 statistical noise for short timescales. Forced symmetrization, by
2845 using the matrix T_sym = 1/2 (T + transpose(T)), removes problems
2846 like the existence of (small magnitude) negative eigenvalues.
2848 .. mdp:: mininum-var-min
2851 The min-variance strategy (option of :mdp:`lmc-stats` is only
2852 valid for larger number of samples, and can get stuck if too few
2853 samples are used at each state. :mdp:`mininum-var-min` is the
2854 minimum number of samples that each state that are allowed before
2855 the min-variance strategy is activated if selected.
2857 .. mdp:: init-lambda-weights
2859 The initial weights (free energies) used for the expanded ensemble
2860 states. Default is a vector of zero weights. format is similar to
2861 the lambda vector settings in :mdp:`fep-lambdas`, except the
2862 weights can be any floating point number. Units are kT. Its length
2863 must match the lambda vector lengths.
2865 .. mdp:: lmc-weights-equil
2869 Expanded ensemble weights continue to be updated throughout the
2874 The input expanded ensemble weights are treated as equilibrated,
2875 and are not updated throughout the simulation.
2877 .. mdp-value:: wl-delta
2879 Expanded ensemble weight updating is stopped when the
2880 Wang-Landau incrementor falls below this value.
2882 .. mdp-value:: number-all-lambda
2884 Expanded ensemble weight updating is stopped when the number of
2885 samples at all of the lambda states is greater than this value.
2887 .. mdp-value:: number-steps
2889 Expanded ensemble weight updating is stopped when the number of
2890 steps is greater than the level specified by this value.
2892 .. mdp-value:: number-samples
2894 Expanded ensemble weight updating is stopped when the number of
2895 total samples across all lambda states is greater than the level
2896 specified by this value.
2898 .. mdp-value:: count-ratio
2900 Expanded ensemble weight updating is stopped when the ratio of
2901 samples at the least sampled lambda state and most sampled
2902 lambda state greater than this value.
2904 .. mdp:: simulated-tempering
2907 Turn simulated tempering on or off. Simulated tempering is
2908 implemented as expanded ensemble sampling with different
2909 temperatures instead of different Hamiltonians.
2911 .. mdp:: sim-temp-low
2914 Low temperature for simulated tempering.
2916 .. mdp:: sim-temp-high
2919 High temperature for simulated tempering.
2921 .. mdp:: simulated-tempering-scaling
2923 Controls the way that the temperatures at intermediate lambdas are
2924 calculated from the :mdp:`temperature-lambdas` part of the lambda
2927 .. mdp-value:: linear
2929 Linearly interpolates the temperatures using the values of
2930 :mdp:`temperature-lambdas`, *i.e.* if :mdp:`sim-temp-low`
2931 =300, :mdp:`sim-temp-high` =400, then lambda=0.5 correspond to
2932 a temperature of 350. A nonlinear set of temperatures can always
2933 be implemented with uneven spacing in lambda.
2935 .. mdp-value:: geometric
2937 Interpolates temperatures geometrically between
2938 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2939 has temperature :mdp:`sim-temp-low` * (:mdp:`sim-temp-high` /
2940 :mdp:`sim-temp-low`) raised to the power of
2941 (i/(ntemps-1)). This should give roughly equal exchange for
2942 constant heat capacity, though of course things simulations that
2943 involve protein folding have very high heat capacity peaks.
2945 .. mdp-value:: exponential
2947 Interpolates temperatures exponentially between
2948 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2949 has temperature :mdp:`sim-temp-low` + (:mdp:`sim-temp-high` -
2950 :mdp:`sim-temp-low`)*((exp(:mdp:`temperature-lambdas`
2951 (i))-1)/(exp(1.0)-i)).
2959 groups for constant acceleration (*e.g.* ``Protein Sol``) all atoms
2960 in groups Protein and Sol will experience constant acceleration as
2961 specified in the :mdp:`accelerate` line
2965 (0) [nm ps\ :sup:`-2`]
2966 acceleration for :mdp:`acc-grps`; x, y and z for each group
2967 (*e.g.* ``0.1 0.0 0.0 -0.1 0.0 0.0`` means that first group has
2968 constant acceleration of 0.1 nm ps\ :sup:`-2` in X direction, second group
2973 Groups that are to be frozen (*i.e.* their X, Y, and/or Z position
2974 will not be updated; *e.g.* ``Lipid SOL``). :mdp:`freezedim`
2975 specifies for which dimension(s) the freezing applies. To avoid
2976 spurious contributions to the virial and pressure due to large
2977 forces between completely frozen atoms you need to use energy group
2978 exclusions, this also saves computing time. Note that coordinates
2979 of frozen atoms are not scaled by pressure-coupling algorithms.
2983 dimensions for which groups in :mdp:`freezegrps` should be frozen,
2984 specify ``Y`` or ``N`` for X, Y and Z and for each group (*e.g.*
2985 ``Y Y N N N N`` means that particles in the first group can move only in
2986 Z direction. The particles in the second group can move in any
2989 .. mdp:: cos-acceleration
2991 (0) [nm ps\ :sup:`-2`]
2992 the amplitude of the acceleration profile for calculating the
2993 viscosity. The acceleration is in the X-direction and the magnitude
2994 is :mdp:`cos-acceleration` cos(2 pi z/boxheight). Two terms are
2995 added to the energy file: the amplitude of the velocity profile and
3000 (0 0 0 0 0 0) [nm ps\ :sup:`-1`]
3001 The velocities of deformation for the box elements: a(x) b(y) c(z)
3002 b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
3003 is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
3004 elements are corrected for periodicity. The coordinates are
3005 transformed accordingly. Frozen degrees of freedom are (purposely)
3006 also transformed. The time ts is set to t at the first step and at
3007 steps at which x and v are written to trajectory to ensure exact
3008 restarts. Deformation can be used together with semiisotropic or
3009 anisotropic pressure coupling when the appropriate
3010 compressibilities are set to zero. The diagonal elements can be
3011 used to strain a solid. The off-diagonal elements can be used to
3012 shear a solid or a liquid.
3018 .. mdp:: electric-field-x
3019 .. mdp:: electric-field-y
3020 .. mdp:: electric-field-z
3022 Here you can specify an electric field that optionally can be
3023 alternating and pulsed. The general expression for the field
3024 has the form of a gaussian laser pulse:
3026 .. math:: E(t) = E_0 \exp\left[-\frac{(t-t_0)^2}{2\sigma^2}\right]\cos\left[\omega (t-t_0)\right]
3028 For example, the four parameters for direction x are set in the
3029 fields of :mdp:`electric-field-x` (and similar for ``electric-field-y``
3030 and ``electric-field-z``) like
3032 ``electric-field-x = E0 omega t0 sigma``
3034 with units (respectively) V nm\ :sup:`-1`, ps\ :sup:`-1`, ps, ps.
3036 In the special case that ``sigma = 0``, the exponential term is omitted
3037 and only the cosine term is used. If also ``omega = 0`` a static
3038 electric field is applied.
3040 Read more at :ref:`electric fields` and in ref. \ :ref:`146 <refCaleman2008a>`.
3043 Mixed quantum/classical molecular dynamics
3044 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
3048 groups to be descibed at the QM level for MiMiC QM/MM
3054 QM/MM is no longer supported via these .mdp options. For MiMic, use no here.
3056 Computational Electrophysiology
3057 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
3058 Use these options to switch on and control ion/water position exchanges in "Computational
3059 Electrophysiology" simulation setups. (See the `reference manual`_ for details).
3065 Do not enable ion/water position exchanges.
3067 .. mdp-value:: X ; Y ; Z
3069 Allow for ion/water position exchanges along the chosen direction.
3070 In a typical setup with the membranes parallel to the x-y plane,
3071 ion/water pairs need to be exchanged in Z direction to sustain the
3072 requested ion concentrations in the compartments.
3074 .. mdp:: swap-frequency
3076 (1) The swap attempt frequency, i.e. every how many time steps the ion counts
3077 per compartment are determined and exchanges made if necessary.
3078 Normally it is not necessary to check at every time step.
3079 For typical Computational Electrophysiology setups, a value of about 100 is
3080 sufficient and yields a negligible performance impact.
3082 .. mdp:: split-group0
3084 Name of the index group of the membrane-embedded part of channel #0.
3085 The center of mass of these atoms defines one of the compartment boundaries
3086 and should be chosen such that it is near the center of the membrane.
3088 .. mdp:: split-group1
3090 Channel #1 defines the position of the other compartment boundary.
3092 .. mdp:: massw-split0
3094 (no) Defines whether or not mass-weighting is used to calculate the split group center.
3098 Use the geometrical center.
3102 Use the center of mass.
3104 .. mdp:: massw-split1
3106 (no) As above, but for split-group #1.
3108 .. mdp:: solvent-group
3110 Name of the index group of solvent molecules.
3112 .. mdp:: coupl-steps
3114 (10) Average the number of ions per compartment over these many swap attempt steps.
3115 This can be used to prevent that ions near a compartment boundary
3116 (diffusing through a channel, e.g.) lead to unwanted back and forth swaps.
3120 (1) The number of different ion types to be controlled. These are during the
3121 simulation exchanged with solvent molecules to reach the desired reference numbers.
3123 .. mdp:: iontype0-name
3125 Name of the first ion type.
3127 .. mdp:: iontype0-in-A
3129 (-1) Requested (=reference) number of ions of type 0 in compartment A.
3130 The default value of -1 means: use the number of ions as found in time step 0
3133 .. mdp:: iontype0-in-B
3135 (-1) Reference number of ions of type 0 for compartment B.
3137 .. mdp:: bulk-offsetA
3139 (0.0) Offset of the first swap layer from the compartment A midplane.
3140 By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers
3141 at maximum distance (= bulk concentration) to the split group layers. However,
3142 an offset b (-1.0 < b < +1.0) can be specified to offset the bulk layer from the middle at 0.0
3143 towards one of the compartment-partitioning layers (at +/- 1.0).
3145 .. mdp:: bulk-offsetB
3147 (0.0) Offset of the other swap layer from the compartment B midplane.
3152 (\1) Only swap ions if threshold difference to requested count is reached.
3156 (2.0) [nm] Radius of the split cylinder #0.
3157 Two split cylinders (mimicking the channel pores) can optionally be defined
3158 relative to the center of the split group. With the help of these cylinders
3159 it can be counted which ions have passed which channel. The split cylinder
3160 definition has no impact on whether or not ion/water swaps are done.
3164 (1.0) [nm] Upper extension of the split cylinder #0.
3168 (1.0) [nm] Lower extension of the split cylinder #0.
3172 (2.0) [nm] Radius of the split cylinder #1.
3176 (1.0) [nm] Upper extension of the split cylinder #1.
3180 (1.0) [nm] Lower extension of the split cylinder #1.
3182 Density-guided simulations
3183 ^^^^^^^^^^^^^^^^^^^^^^^^^^
3185 These options enable and control the calculation and application of additional
3186 forces that are derived from three-dimensional densities, e.g., from cryo
3187 electron-microscopy experiments. (See the `reference manual`_ for details)
3189 .. mdp:: density-guided-simulation-active
3191 (no) Activate density-guided simulations.
3193 .. mdp:: density-guided-simulation-group
3195 (protein) The atoms that are subject to the forces from the density-guided
3196 simulation and contribute to the simulated density.
3198 .. mdp:: density-guided-simulation-similarity-measure
3200 (inner-product) Similarity measure between the density that is calculated
3201 from the atom positions and the reference density.
3203 .. mdp-value:: inner-product
3205 Takes the sum of the product of reference density and simulated density
3208 .. mdp-value:: relative-entropy
3210 Uses the negative relative entropy (or Kullback-Leibler divergence)
3211 between reference density and simulated density as similarity measure.
3212 Negative density values are ignored.
3214 .. mdp-value:: cross-correlation
3216 Uses the Pearson correlation coefficient between reference density and
3217 simulated density as similarity measure.
3219 .. mdp:: density-guided-simulation-atom-spreading-weight
3221 (unity) Determines the multiplication factor for the Gaussian kernel when
3222 spreading atoms on the grid.
3224 .. mdp-value:: unity
3226 Every atom in the density fitting group is assigned the same unit factor.
3230 Atoms contribute to the simulated density proportional to their mass.
3232 .. mdp-value:: charge
3234 Atoms contribute to the simulated density proportional to their charge.
3236 .. mdp:: density-guided-simulation-force-constant
3238 (1e+09) [kJ mol\ :sup:`-1`] The scaling factor for density-guided simulation
3239 forces. May also be negative.
3241 .. mdp:: density-guided-simulation-gaussian-transform-spreading-width
3243 (0.2) [nm] The Gaussian RMS width for the spread kernel for the simulated
3246 .. mdp:: density-guided-simulation-gaussian-transform-spreading-range-in-multiples-of-width
3248 (4) The range after which the gaussian is cut off in multiples of the Gaussian
3249 RMS width described above.
3251 .. mdp:: density-guided-simulation-reference-density-filename
3253 (reference.mrc) Reference density file name using an absolute path or a path
3254 relative to the to the folder from which :ref:`gmx mdrun` is called.
3256 .. mdp:: density-guided-simulation-nst
3258 (1) Interval in steps at which the density fitting forces are evaluated
3259 and applied. The forces are scaled by this number when applied (See the
3260 `reference manual`_ for details).
3262 .. mdp:: density-guided-simulation-normalize-densities
3264 (true) Normalize the sum of density voxel values to one for the reference
3265 density as well as the simulated density.
3267 .. mdp:: density-guided-simulation-adaptive-force-scaling
3269 (false) Adapt the force constant to ensure a steady increase in similarity
3270 between simulated and reference density.
3274 Do not use adaptive force scaling.
3278 Use adaptive force scaling.
3280 .. mdp:: density-guided-simulation-adaptive-force-scaling-time-constant
3282 (4) [ps] Couple force constant to increase in similarity with reference density
3283 with this time constant. Larger times result in looser coupling.
3285 .. mdp:: density-guided-simulation-shift-vector
3287 (0,0,0) [nm] Add this vector to all atoms in the
3288 density-guided-simulation-group before calculating forces and energies for
3289 density-guided-simulations. Affects only the density-guided-simulation forces
3290 and energies. Corresponds to a shift of the input density in the opposite
3291 direction by (-1) * density-guided-simulation-shift-vector.
3293 .. mdp:: density-guided-simulation-transformation-matrix
3295 (1,0,0,0,1,0,0,0,1) Multiply all atoms with this matrix in the
3296 density-guided-simulation-group before calculating forces and energies for
3297 density-guided-simulations. Affects only the density-guided-simulation forces
3298 and energies. Corresponds to a transformation of the input density by the
3299 inverse of this matrix. The matrix is given in row-major order.
3300 This option allows, e.g., rotation of the density-guided atom group around the
3301 z-axis by :math:`\theta` degress by using following input:
3302 :math:`(\cos \theta , -\sin \theta , 0 , \sin \theta , \cos \theta , 0 , 0 , 0 , 1)` .
3304 User defined thingies
3305 ^^^^^^^^^^^^^^^^^^^^^
3309 .. mdp:: userint1 (0)
3310 .. mdp:: userint2 (0)
3311 .. mdp:: userint3 (0)
3312 .. mdp:: userint4 (0)
3313 .. mdp:: userreal1 (0)
3314 .. mdp:: userreal2 (0)
3315 .. mdp:: userreal3 (0)
3316 .. mdp:: userreal4 (0)
3318 These you can use if you modify code. You can pass integers and
3319 reals and groups to your subroutine. Check the inputrec definition
3320 in ``src/gromacs/mdtypes/inputrec.h``
3325 These features have been removed from |Gromacs|, but so that old
3326 :ref:`mdp` and :ref:`tpr` files cannot be mistakenly misused, we still
3327 parse this option. :ref:`gmx grompp` and :ref:`gmx mdrun` will issue a
3328 fatal error if this is set.
3334 .. mdp:: implicit-solvent
3338 .. _reference manual: gmx-manual-parent-dir_