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  15 <h1>mdp options</h1>
  16
  17 <IMG SRC="../gif/rainbow.gif" WIDTH=100% HEIGHT=7>
  18 <P>
  19
  20 <H3>Table of Contents:</H3>
  21
  22 <ul>
  23 <li><A HREF="#general"><b>General remarks</b></A>
  24 <P>
  25 <li><A HREF="#pp"><b>preprocessing</b></A> (title, warnings, cpp, include, define)
  26 <li><A HREF="#run"><b>run control</b></A> (integrator, tinit, dt, nsteps, nstcomm)
  27 <li><A HREF="#ld"><b>langevin dynamics</b></A> (ld_temp, ld_fric, ld_seed)
  28 <li><A HREF="#em"><b>energy minimization</b></A> (emtol, emstep, nstcgsteep)
  29 <li><A HREF="#out"><b>output control</b></A> (nstxout, nstvout, nstfout, nstlog, nstenergy, nstxtcout, xtc_precision, xtc_grps, energygrps)
  30 <li><A HREF="#nl"><b>neighbor searching</b></A> (nstlist, ns_type, deltagrid, box, rlist)
  31 <li><A HREF="#el"><b>electrostatics and VdW</b></A> (coulombtype, rcoulomb_switch, rcoulomb, vdwtype, rvdw_switch, rvdw, epsilon_r, bDispCorr, fourierspacing, fourier_nx, fourier_ny, fourier_nz, pme_order, ewald_rtol, optimize_fft)
  32 <li><A HREF="#tc"><b>Temperature coupling</b></A> (tcoupl, tc_grps, tau_t, ref_t)
  33 <li><A HREF="#pc"><b>Pressure coupling</b></A> (pcoupl, tau_p, compressibility, ref_p)
  34 <li><A HREF="#sa"><b>simulated annealing</b></A> (annealing, zero_temp_time)
  35 <li><A HREF="#vel"><b>velocity generation</b></A> (gen_vel, gen_temp, gen_seed)
  36 <li><A HREF="#sol"><b>solvent optimization</b></A> (solvent_optimization)
  37 <li><A HREF="#bond"><b>bonds</b></A> (constraints, constraint_algorithm, unconstrained_start, shake_tol, lincs_order, lincs_warnangle, nstlincsout, morse)
  38 <li><A HREF="#nmr"><b>NMR refinement</b></A> (disre, disre_weighting, disre_mixed, disre_fc, disre_tau, nstdisreout)
  39 <li><A HREF="#free"><b>Free Energy Perturbation</b></A> (free_energy, init_lambda, delta_lambda)
  40 <li><A HREF="#neq"><b>Non-equilibrium MD</b></A> (acc_grps, accelerate, freezegrps, freezedim )
  41 <li><A HREF="#ef"><b>Electric fields</b></A> (E_x, E_xt, E_y, E_yt, E_z, E_zt )
  42 <li><A HREF="#user"><b>User defined thingies</b></A> (user1_grps, user2_grps, user3_grps, userint1, userint2, userint3, userint4, userreal1, userreal2, userreal3, userreal4)
  43 <li><A HREF="#idx">Index</b></A>
  44 </ul>
  45 </P>
  46
  47 <IMG SRC="../gif/rainbow.gif" WIDTH=100% HEIGHT=7>
  48
  49 <A NAME="general"><br>
  50 <h3>General</h3>
  51
  52 <P>
  53 Default values are given in parentheses. The first option is
  54 always the default option. Units are given in square brackets The
  55 difference between a dash and an underscore is ignored. </P>
  56
  57 <P>
  58 A <a href="mdp.html">sample <TT>.mdp</TT> file</a> is
  59 available. This should be appropriate to start a normal
  60 simulation. Edit it to suit your specific needs and desires. </P>
  61
  62 <A NAME="pp"><br>
  63 <hr>
  64 <h3>Preprocessing</h3>
  65
  66 <dl>
  67 <dt><h4>title:</h4>
  68 <dd>this is redundant, so you can type anything you want
  69 <dt><h4>cpp: </b>(/lib/cpp)</h4>
  70 <dd>your preprocessor
  71 <dt><h4>include:</h4>
  72 <dd>directories to include in your topology. format:
  73 <PRE>-I/home/john/my_lib -I../more_lib</PRE>
  74 <dt><h4>define: </b>()</h4>
  75 <dd>defines to pass to the preprocessor, default is no defines. You can use
  76 any defines to control options in your customized topology files. Options
  77 that are already available by default are:
  78 <dd><dl compact>
  79 <dt><b>-DFLEX_SPC</b>
  80 <dd>Will tell grompp to include FLEX_SPC in stead of SPC into your
  81 topology, this is necessary to make
  82 <b><A HREF="#run">conjugate gradient</A></b> work and will allow
  83 <b><A HREF="#run">steepest descent</A></b> to minimize further.
  84 <dt><b>-DPOSRE</b>
  85 <dd>Will tell grompp to include posre.itp into your topology, used for
  86 <!--Idx-->position restraints<!--EIdx-->.
  87 </dl>
  88 </dl>
  89
  90 <A NAME="run"><br>
  91 <hr>
  92 <h3>Run control</h3>
  93
  94 <dl>
  95 <dt><h4>integrator:</h4>
  96 <dd><dl compact>
  97 <dt><b>md</b>
  98 <dd>A <!--Idx-->leap-frog<!--EIdx--> algorithm for integrating Newton's
  99 equations.
 100 <dt><b>steep</b>
 101 <dd>A <!--Idx-->steepest descent<!--EIdx--> algorithm for energy
 102 minimization. The maximum step size is <b><A HREF="#em">emstep</A></b>
 103 [nm], the tolerance is <b><A HREF="#em">emtol</A></b> [kJ
 104 mol<sup>-1</sup> nm<sup>-1</sup>].
 105 <dt><b>cg</b>
 106 <dd> A <!--Idx-->conjugate gradient<!--EIdx--> algorithm for energy
 107 minimization, the tolerance is <b>emtol</b> [kJ mol<sup>-1</sup>
 108 nm<sup>-1</sup>].  CG is more efficient when a steepest descent step
 109 is done every once in a while, this is determined by
 110 <b><A HREF="#em">nstcgsteep</A></b>.
 111 <dt><b>ld</b>
 112 <dd> An Euler integrator for position Langevin dynamics, the
 113 velocity is the force divided by a friction coefficient
 114 (<b><A HREF="#ld">ld_fric</A></b> [amu ps<sup>-1</sup>])
 115 plus random thermal noise (<b><A HREF="#ld">ld_temp</A></b> [K]).
 116 The random generator is initialized with <b><A HREF="#ld">ld_seed</A></b>
 117 </dl>
 118
 119 <dt><h4>tinit: </b>(0) [ps]</h4>
 120 <dd>starting time for your run (only makes sense for integrators <b>md</b>
 121 and <b>ld</b>)
 122 <dt><h4>dt: </b>(0.001) [ps]</h4>
 123 <dd>time step for integration (only makes sense for integrators <b>md</b>
 124 and <b>ld</b>)
 125 <dt><h4>nsteps: </b>(1)</h4>
 126 <dd>maximum number of steps to integrate
 127 <dt><h4>nstcomm: </b>(1) [steps]</h4>
 128 <dd>if positive: frequency for center of mass motion removal
 129 <dd>if negative: frequency for center of mass motion and rotational
 130 motion removal (should only be used for vacuum simulations)
 131 </dl>
 132
 133 <A NAME="ld"><br>
 134 <hr>
 135 <h3><!--Idx-->Langevin dynamics<!--EIdx--></h3>
 136
 137 <dl>
 138 <dt><h4>ld_temp: </b>(300) [K]</h4>
 139 <dd>temperature in ld run (controls thermal noise level)
 140 <dt><h4>ld_fric: </b>(0) [amu ps<sup>-1</sup>]</h4>
 141 <dd>ld friction coefficient
 142 <dt><h4>ld_seed: </b>(1993) [integer]</h4>
 143 <dd>used to initialize random generator for thermal noise
 144 <dd>when <b>ld_seed</b> is set to -1, the seed is calculated as
 145 <tt>(time() + getpid()) % 65536</tt>
 146 </dl>
 147
 148 <A NAME="em"><br>
 149 <hr>
 150 <h3><!--Idx-->Energy minimization<!--EIdx--></h3>
 151 <dl>
 152 <dt><h4>emtol: </b>(100.0) [kJ mol<sup>-1</sup> nm<sup>-1</sup>]</h4>
 153 <dd>the minimization is converged when the maximum force is smaller than
 154 this value
 155 <dt><h4>emstep: </b>(0.01) [nm]</h4>
 156 <dd>initial step-size
 157 <dt><h4>nstcgsteep: </b>(1000) [steps]</h4>
 158 <dd>frequency of performing 1 steepest descent step while doing
 159 conjugate gradient energy minimization.
 160 </dl>
 161
 162 <A NAME="out"><br>
 163 <hr>
 164 <h3>Output control</h3>
 165 <dl>
 166 <dt><h4>nstxout: </b>(100) [steps]</h4>
 167 <dd>frequency to write coordinates to output
 168 <!--Idx-->trajectory file<!--EIdx-->, the last coordinates are always written
 169 <dt><h4>nstvout: </b>(100) [steps]</h4>
 170 <dd>frequency  to write velocities to output trajectory,
 171 the last velocities are always written
 172 <dt><h4>nstfout: </b>(0) [steps]</h4>
 173 <dd>frequency to write forces to output trajectory.
 174 <dt><h4>nstlog: </b>(100) [steps]</h4>
 175 <dd>frequency to write energies to <!--Idx-->log file<!--EIdx-->,
 176 the last energies are always written
 177 <dt><h4>nstenergy: </b>(100) [steps]</h4>
 178 <dd>frequency to write energies to energy file,
 179 the last energies are always written
 180 <dt><h4>nstxtcout: </b>(0) [steps]</h4>
 181 <dd>frequency to write coordinates to xtc trajectory
 182 <dt><h4>xtc_precision: </b>(1000) [real]</h4>
 183 <dd>precision to write to xtc trajectory
 184 <dt><h4>xtc_grps:</h4>
 185 <dd>group(s) to write to xtc trajectory, default the whole system is written
 186 (if <b>nstxtcout</b> is larger than zero)
 187 <dt><h4>energygrps:</h4>
 188 <dd>group(s) to write to energy file
 189 </dl>
 190
 191 <A NAME="nl"><br>
 192 <hr>
 193 <h3><!--Idx-->Neighbor searching<!--EIdx--></h3>
 194 <dl>
 195 <dt><h4>nstlist: </b>(10) [steps]</h4>
 196 <dd>frequency to update <!--Idx-->neighborlist<!--EIdx-->
 197
 198 <dt><h4>ns_type:</h4>
 199 <dd><dl compact>
 200 <dt><b>grid</b>
 201 <dd>Make a grid in the box and only check atoms in neighboring grid
 202 cells when constructing a new neighbor list every <b>nstlist</b> steps.
 203 The number of grid cells per Coulomb cut-off
 204 length is set with <b>deltagrid</b>, this number should be 2 or 3 for
 205 optimal performance.  In large systems grid search is much faster than
 206 simple search.
 207 <dt><b>simple</b>
 208 <dd>Check every atom in the box when constructing a new neighbor list
 209 every <b>nstlist</b> steps.
 210 </dl>
 211 <dt><h4>deltagrid: </b>(2)</h4>
 212 <dd>number of grid cells per largest cut-off distance
 213
 214 <dt><h4>box:</h4>
 215 <dd><dl compact>
 216 <dt><b>rectangular</b>
 217 <dd>Selects a rectangular box shape.
 218 <dt><b>none</b>
 219 <dd>Selects no box, for use in vacuum simulations.
 220 </dl>
 221
 222 <dt><h4>rlist: </b>(1) [nm]</h4>
 223 <dd>cut-off distance for making the neighbor list
 224 </dl>
 225
 226
 227 <A NAME="el"><br>
 228 <hr>
 229 <h3><!--Idx-->Electrostatics<!--EIdx--> and VdW</h3>
 230 <dl>
 231 <dt><h4>coulombtype:</h4>
 232 <dd><dl compact>
 233
 234 <dt><b>Cut-off</b>
 235 <dd>Twin range cut-off's with neighborlist cut-off <b>rlist</b> and
 236 Coulomb cut-off <b>rcoulomb</b>,
 237 where <b>rlist</b> <tt>&lt=</tt> <b>rvdw</b> <tt>&lt=</tt> <b>rcoulomb</b>.
 238 The dielectric constant is set with <b>epsilon_r</b>.
 239
 240 <dt><b>Ewald</b>
 241 <dd>Classical <!--Idx-->Ewald sum<!--EIdx--> electrostatics.
 242 Use e.g. <b>rlist</b>=0.9,
 243 <b>rvdw</b>=0.9, <b>rcoulomb</b>=0.9. The highest magnitude of
 244 wave vectors used in reciprocal space is controlled by <b>fourierspacing</b>.
 245 The relative accuracy of direct/reciprocal space
 246 is controlled by <b>ewald_rtol</b>. NOTE: Ewald scales as O(N<sup>3/2</sup>)) and
 247 is thus extremely slow for large systems. It is included mainly for
 248 reference - in most cases PME will perform much better.
 249
 250 <dt><b><!--Idx-->PME<!--EIdx--></b>
 251 <dd>Fast Particle-Mesh Ewald electrostatics. Direct space is similar
 252 to the Ewald sum, while the reciprocal part is performed with
 253 FFTs. Grid dimensions are controlled with <b>fourierspacing</b> and the
 254 interpolation order with <b>pme_order</b>. With a grid spacing of 0.1
 255 nm and cubic interpolation the electrostatic forces have an accuracy
 256 of 2-3e-4. Since the error from the vdw-cutoff is larger than this you
 257 might try 0.15 nm. When running in parallel the interpolation
 258 parallelizes better than the FFT, so try decreasing grid dimensions
 259 while increasing interpolation.
 260
 261 <dt><b><!--Idx-->PPPM<!--EIdx--></b>
 262 <dd>Particle-Particle Particle-Mesh algorithm for long range
 263 electrostatic interactions.
 264 Use for example <b>rlist</b><tt>=1.0</tt>, <b>rcoulomb_switch</b><tt>=0.0</TT>,
 265 <b>rcoulomb</b><tt>=0.85</TT>, <b>rvdw_switch</b><tt>=1.0</TT>
 266 and <b>rvdw</b><tt>=1.0</TT>. The grid
 267 dimensions are controlled by <b>fourierspacing</b>.
 268 Reasonable grid spacing for PPPM is 0.05-0.1 nm.
 269 See <tt>Shift</tt> for the details of the particle-particle potential.
 270 NOTE: the pressure in incorrect when using PPPM.
 271
 272 <dt><b><!--Idx-->Reaction-Field<!--EIdx--></b>
 273 <dd>Reaction field with Coulomb cut-off <b>rcoulomb</b>,
 274 where <b>rcoulomb</b> <tt>&gt=</tt> <b>rvdw</b> <tt>&gt=</tt> <b>rlist</b>.
 275 The dielectric constant beyond the cut-off is <b>epsilon_r</b>.
 276 The dielectric constant can be set to infinity by setting <b>epsilon_r</b>=0.
 277
 278 <dt><b>Generalized-Reaction-Field</b>
 279 <dd>Generalized reaction field with Coulomb cut-off <b>rcoulomb</b>,
 280 where <b>rcoulomb</b> <tt>&gt=</tt> <b>rvdw</b> <tt>&gt=</tt> <b>rlist</b>.
 281 The dielectric constant beyond the cut-off is <b>epsilon_r</b>.
 282 The ionic strength is computed from the number of charged
 283 (i.e. with non zero charge) <!--Idx-->charge group<!--EIdx-->s.
 284 The temperature for the GRF potential is set with
 285 <b><A HREF="#tc">ref_t</A></b> [K].
 286 <dt><b>Shift</b>
 287 <dd>The Coulomb
 288 potential is decreased over the whole range and the forces decay smoothly
 289 to zero between <b>rcoulomb_switch</b> and <b>rcoulomb</b>.
 290 The neighbor search cut-off <b>rlist</b> should be 0.1 to 0.3 nm larger than
 291 <b>rcoulomb</b> to accommodate for the size of charge groups and diffusion
 292 between neighbor list updates.
 293
 294 <dt><b>User</b>
 295 <dd>Specify <b>rshort</b> and <b>rlong</b> to the same value, <tt>mdrun</tt>
 296 will now expect to find a file <tt>ctab.xvg</tt> with user-defined functions.
 297 This files should contain 5 columns:
 298 the <tt>x</tt> value, and the function value with its 1<sup>st</sup>
 299 to 3<sup>rd</sup> derivative. The <tt>x</tt> should run from 0 [nm] to
 300 <b>rlist</b><tt>+0.5</tt> [nm], with a spacing of <tt>0.002</tt>
 301 [nm] when you run in single precision, or <tt>0.0005</tt> [nm] when
 302 you run in double precision. The function value at <tt>x=0</tt> is not
 303 important.
 304
 305 </dl>
 306 <A NAME="el2">
 307 <dt><h4>rcoulomb_switch: </b>(0) [nm]</h4>
 308 <dd>where to start switching the Coulomb potential
 309
 310 <dt><h4>rcoulomb: </b>(1) [nm]</h4>
 311 <dd>distance for the Coulomb <!--Idx-->cut-off<!--EIdx-->
 312
 313 <dt><h4>epsilon_r: </b>(1)</h4>
 314 <dd><!--Idx-->dielectric constant<!--EIdx-->
 315
 316 <dt><h4>vdwtype:</h4>
 317 <dd><dl compact>
 318 <dt><b>Cut-off</b>
 319 <dd>Twin range cut-off's with neighbor list cut-off <b>rlist</b> and
 320 VdW cut-off <b>rvdw</b>,
 321 where <b>rvdw</b> <tt>&gt=</tt> <b>rlist</b>.
 322 <dt><b>Shift</b>
 323 <dd>The LJ (not Buckingham) potential is decreased over the whole
 324 range and the forces decay smoothly to zero between <b>rvdw_switch</b>
 325 and <b>rvdw</b>.  The neighbor search cut-off <b>rlist</b> should be
 326 0.1 to 0.3 nm larger than <b>rvdw</b> to accommodate for the size of
 327 charge groups and diffusion between neighbor list
 328 updates.
 329
 330 <dt><b>User</b>
 331 <dd><tt>mdrun</tt> will now expect to find two files with user-defined
 332 functions: <tt>rtab.xvg</tt> for Repulsion, <tt>dtab.xvg</tt> for
 333 Dispersion. These files should contain 5 columns:
 334 the <tt>x</tt> value, and the function value with its 1<sup>st</sup>
 335 to 3<sup>rd</sup> derivative. The <tt>x</tt> should run from 0 [nm] to
 336 <b>rvdw</b><tt>+0.5</tt> [nm], with a spacing of <tt>0.002</tt>
 337 [nm] when you run in single precision, or <tt>0.0005</tt> [nm] when
 338 you run in double precision. The function value at <tt>x=0</tt> is not
 339 important. When you want to use LJ correction, make sure that <b>rvdw</b>
 340 corresponds to the cut-off in the user-defined function.
 341 </dl>
 342
 343 <dt><h4>rvdw_switch: </b>(0) [nm]</h4>
 344 <dd>where to start switching the LJ potential
 345
 346 <dt><h4>rvdw: </b>(1) [nm]</h4>
 347 <dd>distance for the LJ or Buckingham <!--Idx-->cut-off<!--EIdx-->
 348
 349 <dt><h4>bDispCorr:</h4>
 350 <dd><dl compact>
 351 <dt><b>no</b>
 352 <dd>don't apply any correction
 353 <dt><b>yes</b>
 354 <dd>apply long range <!--Idx-->dispersion correction<!--EIdx-->s for Energy
 355 and Pressure
 356 </dl>
 357
 358 <dt><h4>fourierspacing: </b>(0.12) [nm]</h4>
 359 <dd>The maximum grid spacing for the FFT grid when using PPPM or PME.
 360 For ordinary Ewald the spacing times the box dimensions determines the
 361 highest magnitude to use in each direction. In all cases
 362 each direction can be overridden by entering a non-zero value for
 363 <b>fourier_n*</b>.
 364
 365 <dt><h4>fourier_nx </b>(0)<b> ; fourier_ny </b>(0)<b> ; fourier_nz: </b>(0)</h4>
 366 <dd>Highest magnitude of wave vectors in reciprocal space when using Ewald.
 367 <dd>Grid size when using PPPM or PME. These values override
 368 <b>fourierspacing</b> per direction. The best choice is powers of
 369 2, 3, 5 and 7. Avoid large primes.
 370
 371 <dt><h4>pme_order </b>(4)<b></h4>
 372 <dd>Interpolation order for PME. 4 equals cubic interpolation. You might try
 373 6/8/10 when running in parallel and simultaneously decrease grid dimension.
 374
 375 <dt><h4>ewald_rtol </b>(1e-5)<b></h4>
 376 <dd>The relative strength of the Ewald-shifted direct potential at the cutoff
 377 is given by <b>ewald_rtol</b>. Decreasing this will give a more accurate
 378 direct sum, but then you need more wave vectors for the reciprocal sum.
 379
 380 <dt><h4>optimize_fft:</h4>
 381 <dd><dl compact>
 382 <dt><b>no</b>
 383 <dd>Don't calculate the optimal FFT plan for the grid at startup.
 384 <dt><b>yes</b>
 385 <dd>Calculate the optimal FFT plan for the grid at startup. This saves a
 386 few percent for long simulations, but takes a couple of minutes
 387 at start.
 388 </dl>
 389
 390 </dl>
 391
 392 <A NAME="tc"><br>
 393 <hr>
 394 <h3><!--Idx-->Temperature coupling<!--EIdx--></h3>
 395
 396 <dl>
 397 <dt><h4>tcoupl:</h4>
 398 <dd><dl compact>
 399 <dt><b>no</b>
 400 <dd>No temperature coupling.
 401 <dt><b>yes</b>
 402 <dd>Temperature coupling with a Berendsen-thermostat to a bath with
 403 temperature <b>ref_t</b> [K], with time constant <b>tau_t</b> [ps].
 404 Several groups can be coupled separately, these are specified in the
 405 <b>tc_grps</b> field separated by spaces.
 406 </dl>
 407
 408 <dt><h4>tc_grps:</h4>
 409 <dd>groups to couple separately to temperature bath
 410 <dt><h4>tau_t: </b>[ps]</h4>
 411 <dd>time constant for coupling (one for each group in tc_grps)
 412 <dt><h4>ref_t: </b>[K]</h4>
 413 <dd>reference temperature for coupling (one for each group in tc_grps)
 414 </dl>
 415
 416 <A NAME="pc"><br>
 417 <hr>
 418 <h3><!--Idx-->Pressure coupling<!--EIdx--></h3>
 419
 420 <dl>
 421 <dt><h4>pcoupl:</h4>
 422 <dd><dl compact>
 423 <dt><b>no</b>
 424 <dd>No pressure coupling. This means a fixed box size.
 425 <dt><b>isotropic</b>
 426 <dd>Pressure coupling with time constant <b>tau_p</b> [ps].
 427 The compressibility and reference pressure are set with
 428 <b>compressibility</b> [bar<sup>-1</sup>] and <b>ref_p</b> [bar], one
 429 value is needed.
 430 <dt><b>semiisotropic</b>
 431 <dd>Pressure coupling which is isotropic in the x and y direction,
 432 but different in the z direction.
 433 This can be useful for membrane simulations.
 434 2 values are needed for x/y and z directions respectively.
 435 <dt><b>anisotropic</b>
 436 <dd>Idem, but 3 values are needed for x, y and z directions respectively.
 437 Beware that isotropic scaling can lead to extreme deformation
 438 of the simulation box.
 439 <dt><b>surface-tension</b>
 440 <dd>Surface tension coupling for surfaces parallel to the xy-plane.
 441 Uses normal pressure coupling for the z-direction, while the surface tension
 442 is coupled to the x/y dimensions of the box.
 443 The first <b>ref_p</b> value is the reference surface tension times
 444 the number of surfaces [bar nm],
 445 the second value is the reference z-pressure [bar].
 446 The two <b>compressibility</b> [bar<sup>-1</sup>] values are the compressibility
 447 in the x/y and z direction respectively.
 448 The value for the z-compressibility should be reasonably accurate since it
 449 influences the converge of the surface-tension, it can also be set to zero
 450 to have a box with constant height.
 451 <dt><b>triclinic</b>
 452 <dd>Not supported yet.
 453 </dl>
 454
 455 <dt><h4>tau_p: </b>(1) [ps]</h4>
 456 <dd>time constant for coupling
 457 <dt><h4>compressibility: </b>[bar<sup>-1</sup>]</h4>
 458 <dd>compressibility (NOTE: this is now really in bar<sup>-1</sup>)
 459 For water at 1 atm and 300 K the compressibility is 4.5e-5 [bar<sup>-1</sup>].
 460 <dt><h4>ref_p: </b>[bar]</h4>
 461 <dd>reference pressure for coupling
 462
 463 </dl>
 464
 465 <A NAME="sa"><br>
 466 <hr>
 467 <h3><!--Idx-->Simulated annealing<!--EIdx--></h3>
 468
 469 <dl>
 470 <dt><h4>annealing:</h4>
 471 <dd><dl compact>
 472 <dt><b>no</b>
 473 <dd>No simulated annealing.
 474 <dt><b>yes</b>
 475 <dd>Simulated annealing to 0 [K] at time <b>zero_temp_time</b> (ps).
 476 Reference temperature for the Berendsen-thermostat is
 477 <b><A HREF="#tc">ref_t</A></b> x (1 - time / <b>zero_temp_time</b>),
 478 time constant is <b>tau_t</b> [ps]. Note that the reference temperature
 479 will not go below 0 [K], i.e. after <b>zero_temp_time</b> (if it is positive)
 480 the reference temperature will be 0 [K]. Negative <b>zero_temp_time</b>
 481 results in heating, which will go on indefinitely.
 482 </dl>
 483 <dt><h4>zero_temp_time: </b>(0) [ps]</h4>
 484 <dd>time at which temperature will be zero (can be negative). Temperature
 485 during the run can be seen as a straight line going through
 486 T=<b><A HREF="#tc">ref_t</A></b> [K] at t=0 [ps], and
 487 T=0 [K] at t=<b>zero_temp_time</b> [ps]. Look in our
 488 <A HREF="../gmxfaq.html#simann">FAQ</A> for a schematic
 489 graph of temperature versus time.
 490 </dl>
 491
 492 <A NAME="vel"><br>
 493 <hr>
 494 <h3>Velocity generation</h3>
 495
 496 <dl>
 497 <dt><h4>gen_vel:</h4>
 498 <dd><dl compact>
 499 <dt><b>no</b>
 500 <dd> Do not generate velocities at startup. The velocities are set to zero
 501 when there are no velocities in the input structure file.
 502 <dt><b>yes</b>
 503 <dd>Generate velocities according to a Maxwell distribution at
 504 temperature <b>gen_temp</b> [K], with random seed <b>gen_seed</b>.
 505 This is only meaningful with integrator <b><A HREF="#run">md</A></b>.
 506 </dl>
 507 <dt><h4>gen_temp: </b>(300) [K]</h4>
 508 <dd>temperature for Maxwell distribution
 509 <dt><h4>gen_seed: </b>(173529) [integer]</h4>
 510 <dd>used to initialize random generator for random velocities
 511 </dl>
 512
 513 <A NAME="sol"><br>
 514 <hr>
 515 <h3>Solvent optimization</h3>
 516
 517 <dl>
 518 <dt><h4>solvent_optimization:</h4>
 519 <dd><dl compact>
 520 <dt><b>&lt;empty&gt;</b>
 521 <dd>Do not use water specific non-bonded optimizations
 522 <dt><b>&lt;solvent molecule name&gt;</b>
 523 <dd>Use water specific non-bonded optimizations. This string should match the
 524 solvent molecule name in your topology. Check your run time to see
 525 if it is faster.
 526 </dl>
 527 </dl>
 528
 529 <A NAME="bond"><br>
 530 <hr>
 531 <h3>Bonds</h3>
 532
 533 <dl>
 534 <dt><h4><!--Idx-->constraints<!--EIdx-->:</h4>
 535 <dd><dl compact>
 536 <dt><b>none</b>
 537 <dd>No constraints, i.e. bonds are represented by a harmonic or a
 538 Morse potential (depending on the setting of <b>morse</b>) and angles
 539 by a harmonic potential.
 540 <dt><b>hbonds</b>
 541 <dd>Only constrain the bonds with H-atoms.
 542 <dt><b>all-bonds</b>
 543 <dd>Constrain all bonds.
 544 <dt><b>h-angles</b>
 545 <dd>Constrain all bonds and constrain the angles that involve H-atoms
 546 by adding bond-constraints.
 547 <dt><b>all-angles</b>
 548 <dd>Constrain all bonds and constrain all angles by adding bond-constraints.
 549 </dl>
 550
 551 <dt><h4>constraint_alg:</h4>
 552 <dd><dl compact>
 553 <dt><b><!--Idx-->lincs<!--EIdx--></b>
 554 <dd>LINear Constraint Solver. The accuracy in set with
 555 <b>lincs_order</b>, which sets the number of matrices in the expansion
 556 for the matrix inversion, 4 is enough for a "normal" MD simulation, 8 is
 557 needed for LD with large time-steps. If a bond rotates more than
 558 <b>lincs_warnangle</b> [degrees] in one step,
 559 a warning will be printed both to the log file and to <TT>stderr</TT>.
 560 Lincs should not be used with coupled angle constraints.
 561 <dt><b><!--Idx-->shake<!--EIdx--></b>
 562 <dd>Shake is slower and less stable than Lincs, but does work with
 563 angle constraints.
 564 The relative tolerance is set with <b>shake_tol</b>, 0.0001 is a good value
 565 for "normal" MD.
 566 </dl>
 567 <dt><h4>unconstrained_start:</h4>
 568 <dd><dl compact>
 569 <dt><b>no</b>
 570 <dd>apply constraints to the start configuration
 571 <dt><b>yes</b>
 572 <dd>do not apply constraints to the start configuration
 573 </dl>
 574
 575 <A NAME="bond2">
 576 <dt><h4>shake_tol: </b>(0.0001)</h4>
 577 <dd>relative tolerance for shake
 578 <dt><h4>lincs_order: </b>(4)</h4>
 579 <dd>Highest order in the expansion of the constraint coupling matrix.
 580 <b>lincs_order</b> is also used for the number of Lincs iterations
 581 during energy minimization, only one iteration is used in MD.
 582 <dt><h4>lincs_warnangle: </b>(30) [degrees]</h4>
 583 <dd>maximum angle that a bond can rotate before Lincs will complain
 584 <dt><h4>nstlincsout: </b>(1000) [steps]</h4>
 585 <dd>frequency to output constraint accuracy in log file
 586
 587 <dt><h4>morse:</h4>
 588 <dd><dl compact>
 589 <dt><b>no</b>
 590 <dd>bonds are represented by a harmonic potential
 591 <dt><b>yes</b>
 592 <dd>bonds are represented by a Morse potential
 593 </dl>
 594 </dl>
 595
 596 <A NAME="nmr"><br>
 597 <hr>
 598 <h3><!--Idx-->NMR refinement<!--EIdx--></h3>
 599 <dl>
 600 <dt><h4>disre:</h4>
 601 <dd><dl compact>
 602 <dt><b>none</b>
 603 <dd>no <!--Idx-->distance restraints<!--EIdx--> (ignore distance
 604 restraints information in topology file)
 605 <dt><b>simple</b>
 606 <dd>simple (per-molecule) distance restraints
 607 <dt><b>ensemble</b>
 608 <dd>distance restraints over an ensemble of molecules
 609 </dl>
 610 <dt><h4>disre_weighting:</h4>
 611 <dd><dl compact>
 612 <dt><b>equal</b>
 613 <dd>divide the restraint force equally over all atom pairs in the restraint
 614 <dt><b>conservative</b>
 615 <dd>the forces are the derivative of the restraint potential,
 616 this results in an r<sup>-7</sup> weighting of the atom pairs
 617 </dl>
 618 <dt><h4>disre_mixed:</h4>
 619 <dd><dl compact>
 620 <dt><b>no</b>
 621 <dd>the violation used in the calculation of the restraint force is the
 622 time averaged violation
 623 <dt><b>yes</b>
 624 <dd>the violation used in the calculation of the restraint force is the
 625 square root of the time averaged violation times the instantaneous violation
 626 </dl>
 627 <dt><h4>disre_fc: </b>(1000) [kJ mol<sup>-1</sup> nm<sup>-2</sup>]</h4>
 628 <dd>force constant for distance restraints, which is multiplied by a
 629 (possibly) different factor for each restraint
 630 <dt><h4>disre_tau: </b>(0) [ps]</h4>
 631 <dd>time constant for distance restraints running average
 632
 633 <dt><h4>nstdisreout: </b>(100) [steps]</h4>
 634 <dd>frequency to write the running time averaged and instantaneous distances
 635 of all atom pairs involved in restraints to the energy file
 636 (can make the energy file very large)
 637 </dl>
 638
 639 <A NAME="free"><br>
 640 <hr>
 641 <h3><!--Idx-->Free Energy Perturbation<!--EIdx--></h3>
 642
 643 <dl>
 644 <dt><h4>free_energy:</h4>
 645 <dd><dl compact>
 646 <dt><b>no</b>
 647 <dd>Only use topology A.
 648 <dt><b>yes</b>
 649 <dd>Change the system from topology A (lambda=0) to topology B (lambda=1)
 650 and calculate the free energy difference.
 651 The starting value of lambda is <b>init_lambda</b> the increase
 652 per time step is <b>delta_lambda</b>.
 653 </dl>
 654 <dt><h4>init_lambda: </b>(0)</h4>
 655 <dd>starting value for lambda
 656 <dt><h4>delta_lambda: </b>(0)</h4>
 657 <dd>increase per time step for lambda
 658 </dl>
 659
 660 <A NAME="neq"><br>
 661 <hr>
 662 <h3><!--Idx-->Non-equilibrium MD<!--EIdx--></h3>
 663
 664 <dl>
 665 <dt><h4>acc_grps: </b></h4>
 666 <dd>groups for constant acceleration (e.g.: <tt>Protein Sol</tt>)
 667 all atoms in groups Protein and Sol will experience constant acceleration
 668 as specified in the <b>accelerate</b> line
 669 <dt><h4>accelerate: </b>(0) [nm ps<sup>-2</sup>]</h4>
 670 <dd>acceleration for <b>acc_grps</b>; x, y and z for each group
 671 (e.g. <tt>0.1 0.0 0.0 -0.1 0.0 0.0</tt> means that first group has constant
 672 acceleration of 0.1 nm ps<sup>-2</sup> in X direction, second group the
 673 opposite).
 674 <dt><h4>freezegrps: </b></h4>
 675 <dd>Groups that are to be frozen (i.e. their X, Y, and/or Z position will
 676 not be updated; e.g. <tt>Lipid SOL</tt>). <b>freezedim</b> specifies for
 677 which dimension the freezing applies.
 678 <dt><h4>freezedim: </b></h4>
 679 <dd>dimensions for which groups in <b>freezegrps</b> should be frozen,
 680 specify <tt>Y</tt> or <tt>N</tt> for X, Y and Z and for each group
 681 (e.g. <tt>Y Y N N N N</tt> means that particles in the first group
 682 can move only in Z direction. The particles in the second group can
 683 move in any direction).
 684 </dl>
 685
 686 <A NAME="ef"><br>
 687 <hr>
 688 <h3><!--Idx-->Electric field<!--EIdx-->s</h3>
 689
 690 <dl>
 691 <dt><h4>E_x ; E_y ; E_z:</h4>
 692 <dd>If you want to use an electric field in a direction, enter 3 numbers
 693 after the appropriate E_*, the first number: the number of cosines,
 694 only 1 is implemented (with frequency 0) so enter 1,
 695 the second number: the strength of the electric field in
 696 <b>V nm<sup>-1</sup></b>,
 697 the third number: the phase of the cosine, you can enter any number here
 698 since a cosine of frequency zero has no phase.
 699 <dt><h4>E_xt </b><b> ;  E_yt </b><b> ;  E_zt: </b></h4>
 700 <dd>not implemented yet
 701 </dl>
 702
 703 <A NAME="user"><br>
 704 <hr>
 705 <h3>User defined thingies</h3>
 706
 707 <dl>
 708 <dt><h4>user1_grps </b><b> ; user2_grps </b><b> ; user3_grps: </b></h4>
 709 <dt><h4>userint1 </b>(0)<b> ; userint2 </b>(0)<b> ; userint3 </b>(0)<b> ; userint4: </b>(0)</h4>
 710 <dt><h4>userreal1 </b>(0)<b> ; userreal2 </b>(0)<b> ; userreal3 </b>(0)<b> ; userreal4: </b>(0)</h4>
 711 <dd>These you can use if you hack out code. You can pass integers and
 712 reals to your subroutine. Check the inputrec definition in
 713 <tt>src/include/types/inputrec.h</tt>
 714
 715 </dl>
 716
 717 <A NAME="idx"><br>
 718 <hr>
 719 <h3>Index</h3>
 720
 721 <P>
 722
 723 <multicol cols=4>
 724 <A HREF="#neq">acc_grps</A><br>
 725 <A HREF="#neq">accelerate</A><br>
 726 <A HREF="#sa">annealing</A><br>
 727 <A HREF="#el2">bDispCorr</A><br>
 728 <A HREF="#nl">box</A><br>
 729 <A HREF="#pc">compressibility</A><br>
 730 <A HREF="#bond">constraint_algorithm</A><br>
 731 <A HREF="#bond">constraints</A><br>
 732 <A HREF="#el">coulombtype</A><br>
 733 <A HREF="#pp">cpp</A><br>
 734 <A HREF="#pp">define</A><br>
 735 <A HREF="#free">delta_lambda</A><br>
 736 <A HREF="#nl">deltagrid</A><br>
 737 <A HREF="#nmr">disre</A><br>
 738 <A HREF="#nmr">disre_weighting</A><br>
 739 <A HREF="#nmr">disre_mixed</A><br>
 740 <A HREF="#nmr">disre_fc</A><br>
 741 <A HREF="#nmr">disre_tau</A><br>
 742 <A HREF="#run">dt</A><br>
 743 <A HREF="#em">emstep</A><br>
 744 <A HREF="#em">emtol</A><br>
 745 <A HREF="#out">energygrps</A><br>
 746 <A HREF="#el2">epsilon_r</A><br>
 747 <A HREF="#el2">ewald_rtol</A><br>
 748 <A HREF="#ef">E_x</A><br>
 749 <A HREF="#ef">E_xt</A><br>
 750 <A HREF="#ef">E_y</A><br>
 751 <A HREF="#ef">E_yt</A><br>
 752 <A HREF="#ef">E_z</A><br>
 753 <A HREF="#ef">E_zt </A><br>
 754 <A HREF="#el2">fourier_nx</A><br>
 755 <A HREF="#el2">fourier_ny</A><br>
 756 <A HREF="#el2">fourier_nz</A><br>
 757 <A HREF="#el2">fourierspacing</A><br>
 758 <A HREF="#free">free_energy</A><br>
 759 <A HREF="#neq">freezedim </A><br>
 760 <A HREF="#neq">freezegrps</A><br>
 761 <A HREF="#vel">gen_seed</A><br>
 762 <A HREF="#vel">gen_temp</A><br>
 763 <A HREF="#vel">gen_vel</A><br>
 764 <A HREF="#pp">include</A><br>
 765 <A HREF="#free">init_lambda</A><br>
 766 <A HREF="#run">integrator</A><br>
 767 <A HREF="#ld">ld_fric</A><br>
 768 <A HREF="#ld">ld_seed</A><br>
 769 <A HREF="#ld">ld_temp</A><br>
 770 <A HREF="#bond2">lincs_order</A><br>
 771 <A HREF="#bond2">lincs_warnangle</A><br>
 772 <A HREF="#bond2">morse</A><br>
 773 <A HREF="#em">nstcgsteep</A><br>
 774 <A HREF="#run">nstcomm</A><br>
 775 <A HREF="#nmr">nstdisreout</A><br>
 776 <A HREF="#out">nstenergy</A><br>
 777 <A HREF="#run">nsteps</A><br>
 778 <A HREF="#out">nstfout</A><br>
 779 <A HREF="#bond2">nstlincsout</A><br>
 780 <A HREF="#nl">nstlist</A><br>
 781 <A HREF="#out">nstlog</A><br>
 782 <A HREF="#out">nstvout</A><br>
 783 <A HREF="#out">nstxout</A><br>
 784 <A HREF="#out">nstxtcout</A><br>
 785 <A HREF="#nl">ns_type</A><br>
 786 <A HREF="#el2">optimize_fft</A><br>
 787 <A HREF="#pc">pcoupl</A><br>
 788 <A HREF="#el2">pme_order</A><br>
 789 <A HREF="#pc">ref_p</A><br>
 790 <A HREF="#tc">ref_t</A><br>
 791 <A HREF="#el2">rlist</A><br>
 792 <A HREF="#el2">rcoulomb_switch</A><br>
 793 <A HREF="#el2">rcoulomb</A><br>
 794 <A HREF="#el2">rvdw_switch</A><br>
 795 <A HREF="#el2">rvdw</A><br>
 796 <A HREF="#bond2">shake_tol</A><br>
 797 <A HREF="#sol">solvent_optimization</A><br>
 798 <A HREF="#pc">tau_p</A><br>
 799 <A HREF="#tc">tau_t</A><br>
 800 <A HREF="#tc">tc_grps</A><br>
 801 <A HREF="#tc">tcoupl</A><br>
 802 <A HREF="#run">tinit</A><br>
 803 <A HREF="#pp">title</A><br>
 804 <A HREF="#bond">unconstrained_start</A><br>
 805 <A HREF="#user">user1_grps</A><br>
 806 <A HREF="#user">user2_grps</A><br>
 807 <A HREF="#user">user3_grps</A><br>
 808 <A HREF="#user">userint1</A><br>
 809 <A HREF="#user">userint2</A><br>
 810 <A HREF="#user">userint3</A><br>
 811 <A HREF="#user">userint4</A><br>
 812 <A HREF="#user">userreal1</A><br>
 813 <A HREF="#user">userreal2</A><br>
 814 <A HREF="#user">userreal3</A><br>
 815 <A HREF="#user">userreal4</A><br>
 816 <A HREF="#el">vdwtype</A><br>
 817 <A HREF="#pp">warnings</A><br>
 818 <A HREF="#out">xtc_grps</A><br>
 819 <A HREF="#out">xtc_precision</A><br>
 820 <A HREF="#sa">zero_temp_time</A><br>
 821 </multicol>
 822
 823 <IMG SRC="../gif/rainbow.gif" WIDTH=100% HEIGHT=7>
 824 <P>
 825
 826 </BODY>
 827 </HTML>
 828