share/html/online/mdp.html

   1 <title>mdp file format</title>
   2 <body>
   3 <h2>mdp file format</h2>
   4
   5 <P> <a href="mdp_opt.html">full description of the options</a>.  </P>
   6
   7 <P> Here is a sample mdp file.
   8 The ordering of the items is not important, but if you enter the same
   9 thing twice, the <b>first</b> is used. Dashes and underscores on the
  10 left hand side are ignored.</P>
  11
  12 <P> The values of the options are reasonable values for a 1 nanosecond
  13 MD run of a protein in a box of water. </P>
  14
  15 <hr>
  16 <pre>
  17 title                    = Yo
  18 cpp                      = /lib/cpp
  19 include                  = -I../top
  20 define                   =
  21 integrator               = md
  22 dt                       = 0.002
  23 nsteps                   = 500000
  24 nstxout                  = 5000
  25 nstvout                  = 5000
  26 nstlog                   = 5000
  27 nstenergy                = 250
  28 nstxtcout                = 250
  29 xtc_grps                 = Protein
  30 energygrps               = Protein  SOL
  31 nstlist                  = 10
  32 ns_type                  = grid
  33 rlist                    = 0.8
  34 coulombtype              = cut-off
  35 rcoulomb                 = 1.4
  36 rvdw                     = 0.8
  37 tcoupl                   = yes
  38 tc-grps                  = Protein      SOL
  39 tau_t                    = 0.1  0.1
  40 ref_t                    = 300  300
  41 Pcoupl                   = isotropic
  42 tau_p                    = 1.0
  43 compressibility          = 4.5e-5
  44 ref_p                    = 1.0
  45 gen_vel                  = yes
  46 gen_temp                 = 300
  47 gen_seed                 = 173529
  48 solvent_optimization     = SOL
  49 constraints              = all-bonds
  50 </pre>
  51 <hr>
  52
  53 <p>
  54 With this input <a href="grompp.html"><tt>grompp</tt></a> will produce
  55 an <tt>mdout.mdp</tt> with all the options and descriptions:
  56 </p>
  57
  58 <hr>
  59 <pre>
  60 ; VARIOUS PREPROCESSING OPTIONS =
  61 title                    = Yo
  62 cpp                      = /lib/cpp
  63 include                  = -I../top
  64 define                   =
  65
  66 ; RUN CONTROL PARAMETERS =
  67 integrator               = md
  68 ; start time and timestep in ps =
  69 tinit                    = 0
  70 dt                       = 0.002
  71 nsteps                   = 500000
  72 ; number of steps for center of mass motion removal =
  73 nstcomm                  = 1
  74
  75 ; LANGEVIN DYNAMICS OPTIONS =
  76 ; Temperature, friction coefficient (amu/ps) and random seed =
  77 ld_temp                  = 300
  78 ld_fric                  = 0
  79 ld_seed                  = 1993
  80
  81 ; ENERGY MINIMIZATION OPTIONS =
  82 ; Force tolerance and initial step-size =
  83 emtol                    = 100
  84 emstep                   = 0.01
  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 nstxtcout                = 250
  98 xtc_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 xtc_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 deltagrid                = 2
 111 ; Box type, rectangular, triclinic, none =
 112 box                      = Rectangular
 113 ; nblist cut-off         =
 114 rlist                    = 0.8
 115
 116 ; OPTIONS FOR ELECTROSTATICS AND VDW =
 117 ; Method for doing electrostatics =
 118 coulombtype              = cut-off
 119 rcoulomb_switch          = 0
 120 rcoulomb                 = 1.4
 121 ; Dielectric constant (DC) for cut-off or DC of reaction field =
 122 epsilon_r                = 1
 123 ; Method for doing Van der Waals =
 124 vdw_type                 = Cut-off
 125 ; cut-off lengths        =
 126 rvdw_switch              = 0
 127 rvdw                     = 0.8
 128 ; Apply long range dispersion corrections for Energy and Pressure =
 129 bDispCorr                = no
 130 ; Spacing for the PME/PPPM FFT grid =
 131 fourierspacing           = 0.12
 132 ; FFT grid size, when a value is 0 fourierspacing will be used =
 133 fourier_nx               = 0
 134 fourier_ny               = 0
 135 fourier_nz               = 0
 136 ; EWALD/PME/PPPM parameters =
 137 pme_order                = 4
 138 ewald_rtol               = 1e-05
 139 optimize_fft             = no
 140
 141 ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
 142 ; Temperature coupling   =
 143 tcoupl                   = yes
 144 ; Groups to couple separately =
 145 tc-grps                  = Protein      SOL
 146 ; Time constant (ps) and reference temperature (K) =
 147 tau_t                    = 0.1  0.1
 148 ref_t                    = 300  300
 149 ; Pressure coupling      =
 150 Pcoupl                   = 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 ; OPTIMIZATIONS FOR SOLVENT MODELS =
 167 ; Solvent molecule name (blank: no optimization) =
 168 solvent_optimization     = SOL
 169
 170 ; OPTIONS FOR BONDS     =
 171 constraints              = all-bonds
 172 ; Type of constraint algorithm =
 173 constraint_algorithm     = Lincs
 174 ; Do not constrain the start configuration =
 175 unconstrained_start      = no
 176 ; Relative tolerance of shake =
 177 shake_tol                = 0.0001
 178 ; Highest order in the expansion of the constraint coupling matrix =
 179 lincs_order              = 4
 180 ; Lincs will write a warning to the stderr if in one step a bond =
 181 ; rotates over more degrees than =
 182 lincs_warnangle          = 30
 183 ; Output frequency of the Lincs accuracy =
 184 nstLincsout              = 1000
 185 ; Convert harmonic bonds to morse potentials =
 186 morse                    = no
 187
 188 ; NMR refinement stuff  =
 189 ; Distance restraints type: No, Simple or Ensemble =
 190 disre                    = No
 191 ; Force weighting of pairs in one distance restraint: Equal or Conservative =
 192 disre_weighting          = Equal
 193 ; Use sqrt of the time averaged times the instantaneous violation =
 194 disre_mixed              = no
 195 disre_fc                 = 1000
 196 disre_tau                = 0
 197 ; Output frequency for pair distances to energy file =
 198 nstdisreout              = 100
 199
 200 ; Free energy control stuff =
 201 free_energy              = no
 202 init_lambda              = 0
 203 delta_lambda             = 0
 204
 205 ; Non-equilibrium MD stuff =
 206 acc_grps                 =
 207 accelerate               =
 208 freezegrps               =
 209 freezedim                =
 210
 211 ; Electric fields       =
 212 ; Format is number of terms (int) and for all terms an amplitude (real) =
 213 ; and a phase angle (real) =
 214 E_x                      =
 215 E_xt                     =
 216 E_y                      =
 217 E_yt                     =
 218 E_z                      =
 219 E_zt                     =
 220
 221 ; User defined thingies =
 222 user1_grps               =
 223 user2_grps               =
 224 user3_grps               =
 225 userint1                 = 0
 226 userint2                 = 0
 227 userint3                 = 0
 228 userint4                 = 0
 229 userreal1                = 0
 230 userreal2                = 0
 231 userreal3                = 0
 232 userreal4                = 0
 233 </pre>
 234 <hr>
 235
 236 </body>