docs/old-html/online/mdp.html

   1 <title>mdp file format</title>
   2 <P> Follow <a href="mdp_opt.html">this link</a> for a detailed description of the options</a>.  </P>
   3
   4 <P> Below is a sample mdp file.
   5 The ordering of the items is not important, but if you enter the same
   6 thing twice, the <b>last</b> is used (grompp gives you a note when
   7 overriding values). Dashes and underscores on the
   8 left hand side are ignored.</P>
   9
  10 <P> The values of the options are reasonable values for a 1 nanosecond
  11 MD run of a protein in a box of water. </P>
  12
  13 <hr>
  14 <pre>
  15 title                    = Yo
  16 cpp                      = /lib/cpp
  17 include                  = -I../top
  18 define                   =
  19 integrator               = md
  20 dt                       = 0.002
  21 nsteps                   = 500000
  22 nstxout                  = 5000
  23 nstvout                  = 5000
  24 nstlog                   = 5000
  25 nstenergy                = 250
  26 nstxout-compressed       = 250
  27 compressed-x-grps        = Protein
  28 energygrps               = Protein  SOL
  29 nstlist                  = 10
  30 ns-type                  = grid
  31 rlist                    = 0.8
  32 coulombtype              = cut-off
  33 rcoulomb                 = 1.4
  34 rvdw                     = 0.8
  35 tcoupl                   = Berendsen
  36 tc-grps                  = Protein      SOL
  37 tau-t                    = 0.1  0.1
  38 ref-t                    = 300  300
  39 Pcoupl                   = Berendsen
  40 tau-p                    = 1.0
  41 compressibility          = 4.5e-5
  42 ref-p                    = 1.0
  43 gen-vel                  = yes
  44 gen-temp                 = 300
  45 gen-seed                 = 173529
  46 constraints              = all-bonds
  47 </pre>
  48 <hr>
  49
  50 <p>
  51 With this input <a href="../programs/gmx-grompp.html"><tt>grompp</tt></a> will produce
  52 an <tt>mdout.mdp</tt> with all the options and descriptions:
  53 </p>
  54
  55 <hr>
  56 <pre>
  57 ; VARIOUS PREPROCESSING OPTIONS =
  58 title                    = Yo
  59 cpp                      = /lib/cpp
  60 include                  = -I../top
  61 define                   =
  62
  63 ; RUN CONTROL PARAMETERS =
  64 integrator               = md
  65 ; start time and timestep in ps =
  66 tinit                    = 0
  67 dt                       = 0.002
  68 nsteps                   = 500000
  69 ; number of steps for center of mass motion removal =
  70 nstcomm                  = 1
  71 comm-grps                =
  72
  73 ; LANGEVIN DYNAMICS OPTIONS =
  74 ; Temperature, friction coefficient (amu/ps) and random seed =
  75 bd-temp                  = 300
  76 bd-fric                  = 0
  77 ld-seed                  = 1993
  78
  79 ; ENERGY MINIMIZATION OPTIONS =
  80 ; Force tolerance and initial step-size =
  81 emtol                    = 100
  82 emstep                   = 0.01
  83 ; Max number of iterations in relax-shells =
  84 niter                    = 20
  85 ; Frequency of steepest descents steps when doing CG =
  86 nstcgsteep               = 1000
  87
  88 ; OUTPUT CONTROL OPTIONS =
  89 ; Output frequency for coords (x), velocities (v) and forces (f) =
  90 nstxout                  = 5000
  91 nstvout                  = 5000
  92 nstfout                  = 0
  93 ; Output frequency for energies to log file and energy file =
  94 nstlog                   = 5000
  95 nstenergy                = 250
  96 ; Output frequency and precision for xtc file =
  97 nstxout-compressed       = 250
  98 compressed-x-precision   = 1000
  99 ; This selects the subset of atoms for the xtc file. You can =
 100 ; select multiple groups. By default all atoms will be written. =
 101 compressed-x-grps        = Protein
 102 ; Selection of energy groups =
 103 energygrps               = Protein  SOL
 104
 105 ; NEIGHBORSEARCHING PARAMETERS =
 106 ; nblist update frequency =
 107 nstlist                  = 10
 108 ; ns algorithm (simple or grid) =
 109 ns-type                  = grid
 110 ; Periodic boundary conditions: xyz or none =
 111 pbc                      = xyz
 112 ; nblist cut-off         =
 113 rlist                    = 0.8
 114
 115 ; OPTIONS FOR ELECTROSTATICS AND VDW =
 116 ; Method for doing electrostatics =
 117 coulombtype              = cut-off
 118 rcoulomb-switch          = 0
 119 rcoulomb                 = 1.4
 120 ; Dielectric constant (DC) for cut-off or DC of reaction field =
 121 epsilon-r                = 1
 122 ; Method for doing Van der Waals =
 123 vdw-type                 = Cut-off
 124 ; cut-off lengths        =
 125 rvdw-switch              = 0
 126 rvdw                     = 0.8
 127 ; Apply long range dispersion corrections for Energy and Pressure =
 128 DispCorr                 = No
 129 ; Spacing for the PME/PPPM FFT grid =
 130 fourierspacing           = 0.12
 131 ; FFT grid size, when a value is 0 fourierspacing will be used =
 132 fourier-nx               = 0
 133 fourier-ny               = 0
 134 fourier-nz               = 0
 135 ; EWALD/PME/PPPM parameters =
 136 pme-order                = 4
 137 ewald-rtol               = 1e-05
 138 epsilon-surface          = 0
 139
 140 ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
 141 ; Temperature coupling   =
 142 tcoupl                   = Berendsen
 143 ; Groups to couple separately =
 144 tc-grps                  = Protein      SOL
 145 ; Time constant (ps) and reference temperature (K) =
 146 tau-t                    = 0.1  0.1
 147 ref-t                    = 300  300
 148 ; Pressure coupling      =
 149 Pcoupl                   = Berendsen
 150 Pcoupltype               = Isotropic
 151 ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
 152 tau-p                    = 1.0
 153 compressibility          = 4.5e-5
 154 ref-p                    = 1.0
 155
 156 ; SIMULATED ANNEALING CONTROL =
 157 annealing                = no
 158 ; Time at which temperature should be zero (ps) =
 159 zero-temp-time           = 0
 160
 161 ; GENERATE VELOCITIES FOR STARTUP RUN =
 162 gen-vel                  = yes
 163 gen-temp                 = 300
 164 gen-seed                 = 173529
 165
 166 ; OPTIONS FOR BONDS     =
 167 constraints              = all-bonds
 168 ; Type of constraint algorithm =
 169 constraint-algorithm     = Lincs
 170 ; Do not constrain the start configuration =
 171 unconstrained-start      = no
 172 ; Relative tolerance of shake =
 173 shake-tol                = 0.0001
 174 ; Highest order in the expansion of the constraint coupling matrix =
 175 lincs-order              = 4
 176 ; Lincs will write a warning to the stderr if in one step a bond =
 177 ; rotates over more degrees than =
 178 lincs-warnangle          = 30
 179 ; Convert harmonic bonds to morse potentials =
 180 morse                    = no
 181
 182 ; NMR refinement stuff  =
 183 ; Distance restraints type: No, Simple or Ensemble =
 184 disre                    = No
 185 ; Force weighting of pairs in one distance restraint: Equal or Conservative =
 186 disre-weighting          = Equal
 187 ; Use sqrt of the time averaged times the instantaneous violation =
 188 disre-mixed              = no
 189 disre-fc                 = 1000
 190 disre-tau                = 0
 191 ; Output frequency for pair distances to energy file =
 192 nstdisreout              = 100
 193
 194 ; Free energy control stuff =
 195 free-energy              = no
 196 init-lambda              = 0
 197 delta-lambda             = 0
 198 sc-alpha                 = 0
 199 sc-sigma                 = 0.3
 200
 201 ; Non-equilibrium MD stuff =
 202 acc-grps                 =
 203 accelerate               =
 204 freezegrps               =
 205 freezedim                =
 206 cos-acceleration         = 0
 207 energygrp-excl           =
 208
 209 ; Electric fields       =
 210 ; Format is number of terms (int) and for all terms an amplitude (real) =
 211 ; and a phase angle (real) =
 212 E-x                      =
 213 E-xt                     =
 214 E-y                      =
 215 E-yt                     =
 216 E-z                      =
 217 E-zt                     =
 218
 219 ; User defined thingies =
 220 user1-grps               =
 221 user2-grps               =
 222 userint1                 = 0
 223 userint2                 = 0
 224 userint3                 = 0
 225 userint4                 = 0
 226 userreal1                = 0
 227 userreal2                = 0
 228 userreal3                = 0
 229 userreal4                = 0
 230 </pre>