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   5 <h2>mdp file format</h2>
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   8 <TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
   9 <TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
  10 <TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
  11 <TD ALIGN=RIGHT><B>Sun 18 Jan 2009</B></TR></TABLE></CENTER><HR>
  12 <P> Follow <a href="mdp_opt.html">this link</a> for a detailed description of the options</a>.  </P>
  13
  14 <P> Below is a sample mdp file.
  15 The ordering of the items is not important, but if you enter the same
  16 thing twice, the <b>last</b> is used (grompp gives you a note when
  17 overriding values). Dashes and underscores on the
  18 left hand side are ignored.</P>
  19
  20 <P> The values of the options are reasonable values for a 1 nanosecond
  21 MD run of a protein in a box of water. </P>
  22
  23 <hr>
  24 <pre>
  25 title                    = Yo
  26 cpp                      = /lib/cpp
  27 include                  = -I../top
  28 define                   =
  29 integrator               = md
  30 dt                       = 0.002
  31 nsteps                   = 500000
  32 nstxout                  = 5000
  33 nstvout                  = 5000
  34 nstlog                   = 5000
  35 nstenergy                = 250
  36 nstxtcout                = 250
  37 xtc_grps                 = Protein
  38 energygrps               = Protein  SOL
  39 nstlist                  = 10
  40 ns_type                  = grid
  41 rlist                    = 0.8
  42 coulombtype              = cut-off
  43 rcoulomb                 = 1.4
  44 rvdw                     = 0.8
  45 tcoupl                   = Berendsen
  46 tc-grps                  = Protein      SOL
  47 tau_t                    = 0.1  0.1
  48 ref_t                    = 300  300
  49 Pcoupl                   = Berendsen
  50 tau_p                    = 1.0
  51 compressibility          = 4.5e-5
  52 ref_p                    = 1.0
  53 gen_vel                  = yes
  54 gen_temp                 = 300
  55 gen_seed                 = 173529
  56 constraints              = all-bonds
  57 </pre>
  58 <hr>
  59
  60 <p>
  61 With this input <a href="grompp.html"><tt>grompp</tt></a> will produce
  62 an <tt>mdout.mdp</tt> with all the options and descriptions:
  63 </p>
  64
  65 <hr>
  66 <pre>
  67 ; VARIOUS PREPROCESSING OPTIONS =
  68 title                    = Yo
  69 cpp                      = /lib/cpp
  70 include                  = -I../top
  71 define                   =
  72
  73 ; RUN CONTROL PARAMETERS =
  74 integrator               = md
  75 ; start time and timestep in ps =
  76 tinit                    = 0
  77 dt                       = 0.002
  78 nsteps                   = 500000
  79 ; number of steps for center of mass motion removal =
  80 nstcomm                  = 1
  81 comm-grps                =
  82
  83 ; LANGEVIN DYNAMICS OPTIONS =
  84 ; Temperature, friction coefficient (amu/ps) and random seed =
  85 bd-temp                  = 300
  86 bd-fric                  = 0
  87 ld-seed                  = 1993
  88
  89 ; ENERGY MINIMIZATION OPTIONS =
  90 ; Force tolerance and initial step-size =
  91 emtol                    = 100
  92 emstep                   = 0.01
  93 ; Max number of iterations in relax_shells =
  94 niter                    = 20
  95 ; Frequency of steepest descents steps when doing CG =
  96 nstcgsteep               = 1000
  97
  98 ; OUTPUT CONTROL OPTIONS =
  99 ; Output frequency for coords (x), velocities (v) and forces (f) =
 100 nstxout                  = 5000
 101 nstvout                  = 5000
 102 nstfout                  = 0
 103 ; Output frequency for energies to log file and energy file =
 104 nstlog                   = 5000
 105 nstenergy                = 250
 106 ; Output frequency and precision for xtc file =
 107 nstxtcout                = 250
 108 xtc-precision            = 1000
 109 ; This selects the subset of atoms for the xtc file. You can =
 110 ; select multiple groups. By default all atoms will be written. =
 111 xtc_grps                 = Protein
 112 ; Selection of energy groups =
 113 energygrps               = Protein  SOL
 114
 115 ; NEIGHBORSEARCHING PARAMETERS =
 116 ; nblist update frequency =
 117 nstlist                  = 10
 118 ; ns algorithm (simple or grid) =
 119 ns_type                  = grid
 120 ; Periodic boundary conditions: xyz or none =
 121 pbc                      = xyz
 122 ; nblist cut-off         =
 123 rlist                    = 0.8
 124 domain-decomposition     = no
 125
 126 ; OPTIONS FOR ELECTROSTATICS AND VDW =
 127 ; Method for doing electrostatics =
 128 coulombtype              = cut-off
 129 rcoulomb-switch          = 0
 130 rcoulomb                 = 1.4
 131 ; Dielectric constant (DC) for cut-off or DC of reaction field =
 132 epsilon-r                = 1
 133 ; Method for doing Van der Waals =
 134 vdw-type                 = Cut-off
 135 ; cut-off lengths        =
 136 rvdw-switch              = 0
 137 rvdw                     = 0.8
 138 ; Apply long range dispersion corrections for Energy and Pressure =
 139 DispCorr                 = No
 140 ; Spacing for the PME/PPPM FFT grid =
 141 fourierspacing           = 0.12
 142 ; FFT grid size, when a value is 0 fourierspacing will be used =
 143 fourier_nx               = 0
 144 fourier_ny               = 0
 145 fourier_nz               = 0
 146 ; EWALD/PME/PPPM parameters =
 147 pme_order                = 4
 148 ewald_rtol               = 1e-05
 149 epsilon_surface          = 0
 150 optimize_fft             = no
 151
 152 ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
 153 ; Temperature coupling   =
 154 tcoupl                   = Berendsen
 155 ; Groups to couple separately =
 156 tc-grps                  = Protein      SOL
 157 ; Time constant (ps) and reference temperature (K) =
 158 tau_t                    = 0.1  0.1
 159 ref_t                    = 300  300
 160 ; Pressure coupling      =
 161 Pcoupl                   = Berendsen
 162 Pcoupltype               = Isotropic
 163 ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
 164 tau_p                    = 1.0
 165 compressibility          = 4.5e-5
 166 ref_p                    = 1.0
 167
 168 ; SIMULATED ANNEALING CONTROL =
 169 annealing                = no
 170 ; Time at which temperature should be zero (ps) =
 171 zero-temp_time           = 0
 172
 173 ; GENERATE VELOCITIES FOR STARTUP RUN =
 174 gen_vel                  = yes
 175 gen_temp                 = 300
 176 gen_seed                 = 173529
 177
 178 ; OPTIONS FOR BONDS     =
 179 constraints              = all-bonds
 180 ; Type of constraint algorithm =
 181 constraint-algorithm     = Lincs
 182 ; Do not constrain the start configuration =
 183 unconstrained-start      = no
 184 ; Relative tolerance of shake =
 185 shake-tol                = 0.0001
 186 ; Highest order in the expansion of the constraint coupling matrix =
 187 lincs-order              = 4
 188 ; Lincs will write a warning to the stderr if in one step a bond =
 189 ; rotates over more degrees than =
 190 lincs-warnangle          = 30
 191 ; Convert harmonic bonds to morse potentials =
 192 morse                    = no
 193
 194 ; NMR refinement stuff  =
 195 ; Distance restraints type: No, Simple or Ensemble =
 196 disre                    = No
 197 ; Force weighting of pairs in one distance restraint: Equal or Conservative =
 198 disre-weighting          = Equal
 199 ; Use sqrt of the time averaged times the instantaneous violation =
 200 disre-mixed              = no
 201 disre-fc                 = 1000
 202 disre-tau                = 0
 203 ; Output frequency for pair distances to energy file =
 204 nstdisreout              = 100
 205
 206 ; Free energy control stuff =
 207 free-energy              = no
 208 init-lambda              = 0
 209 delta-lambda             = 0
 210 sc-alpha                 = 0
 211 sc-sigma                 = 0.3
 212
 213 ; Non-equilibrium MD stuff =
 214 acc-grps                 =
 215 accelerate               =
 216 freezegrps               =
 217 freezedim                =
 218 cos-acceleration         = 0
 219 energygrp_excl           =
 220
 221 ; Electric fields       =
 222 ; Format is number of terms (int) and for all terms an amplitude (real) =
 223 ; and a phase angle (real) =
 224 E-x                      =
 225 E-xt                     =
 226 E-y                      =
 227 E-yt                     =
 228 E-z                      =
 229 E-zt                     =
 230
 231 ; User defined thingies =
 232 user1-grps               =
 233 user2-grps               =
 234 userint1                 = 0
 235 userint2                 = 0
 236 userint3                 = 0
 237 userint4                 = 0
 238 userreal1                = 0
 239 userreal2                = 0
 240 userreal3                = 0
 241 userreal4                = 0
 242 </pre>
 243
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