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>
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>
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>
26 nstxout-compressed = 250
27 compressed-x-grps = Protein
28 energygrps = Protein SOL
41 compressibility = 4.5e-5
46 constraints = all-bonds
51 With this input <a href="grompp.html"><tt>grompp</tt></a> will produce
52 an <tt>mdout.mdp</tt> with all the options and descriptions:
57 ; VARIOUS PREPROCESSING OPTIONS =
63 ; RUN CONTROL PARAMETERS =
65 ; start time and timestep in ps =
69 ; number of steps for center of mass motion removal =
73 ; LANGEVIN DYNAMICS OPTIONS =
74 ; Temperature, friction coefficient (amu/ps) and random seed =
79 ; ENERGY MINIMIZATION OPTIONS =
80 ; Force tolerance and initial step-size =
83 ; Max number of iterations in relax-shells =
85 ; Frequency of steepest descents steps when doing CG =
88 ; OUTPUT CONTROL OPTIONS =
89 ; Output frequency for coords (x), velocities (v) and forces (f) =
93 ; Output frequency for energies to log file and energy file =
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
105 ; NEIGHBORSEARCHING PARAMETERS =
106 ; nblist update frequency =
108 ; ns algorithm (simple or grid) =
110 ; Periodic boundary conditions: xyz or none =
114 domain-decomposition = no
116 ; OPTIONS FOR ELECTROSTATICS AND VDW =
117 ; Method for doing electrostatics =
118 coulombtype = cut-off
121 ; Dielectric constant (DC) for cut-off or DC of reaction field =
123 ; Method for doing Van der Waals =
128 ; Apply long range dispersion corrections for Energy and Pressure =
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 =
136 ; EWALD/PME/PPPM parameters =
142 ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
143 ; Temperature coupling =
145 ; Groups to couple separately =
146 tc-grps = Protein SOL
147 ; Time constant (ps) and reference temperature (K) =
150 ; Pressure coupling =
152 Pcoupltype = Isotropic
153 ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
155 compressibility = 4.5e-5
158 ; SIMULATED ANNEALING CONTROL =
160 ; Time at which temperature should be zero (ps) =
163 ; GENERATE VELOCITIES FOR STARTUP RUN =
168 ; OPTIONS FOR BONDS =
169 constraints = all-bonds
170 ; Type of constraint algorithm =
171 constraint-algorithm = Lincs
172 ; Do not constrain the start configuration =
173 unconstrained-start = no
174 ; Relative tolerance of shake =
176 ; Highest order in the expansion of the constraint coupling matrix =
178 ; Lincs will write a warning to the stderr if in one step a bond =
179 ; rotates over more degrees than =
181 ; Convert harmonic bonds to morse potentials =
184 ; NMR refinement stuff =
185 ; Distance restraints type: No, Simple or Ensemble =
187 ; Force weighting of pairs in one distance restraint: Equal or Conservative =
188 disre-weighting = Equal
189 ; Use sqrt of the time averaged times the instantaneous violation =
193 ; Output frequency for pair distances to energy file =
196 ; Free energy control stuff =
203 ; Non-equilibrium MD stuff =
212 ; Format is number of terms (int) and for all terms an amplitude (real) =
213 ; and a phase angle (real) =
221 ; User defined thingies =