1 <title>mdp file format</title>
3 for a detailed description of the options</a>. </P>
5 <P> Below is a sample mdp file.
6 The ordering of the items is not important, but if you enter the same
7 thing twice, the <b>last</b> is used (grompp gives you a note when
8 overriding values). Dashes and underscores on the
9 left hand side are ignored.</P>
11 <P> The values of the options are reasonable values for a 1 nanosecond
12 MD run of a protein in a box of water. </P>
27 nstxout-compressed = 250
28 compressed-x-grps = Protein
29 energygrps = Protein SOL
42 compressibility = 4.5e-5
47 constraints = all-bonds
52 With this input <a href="../programs/gmx-grompp.html"><tt>grompp</tt></a> will produce
53 an <tt>mdout.mdp</tt> with all the options and descriptions:
58 ; VARIOUS PREPROCESSING OPTIONS =
64 ; RUN CONTROL PARAMETERS =
66 ; start time and timestep in ps =
70 ; number of steps for center of mass motion removal =
74 ; LANGEVIN DYNAMICS OPTIONS =
75 ; Temperature, friction coefficient (amu/ps) and random seed =
80 ; ENERGY MINIMIZATION OPTIONS =
81 ; Force tolerance and initial step-size =
84 ; Max number of iterations in relax-shells =
86 ; Frequency of steepest descents steps when doing CG =
89 ; OUTPUT CONTROL OPTIONS =
90 ; Output frequency for coords (x), velocities (v) and forces (f) =
94 ; Output frequency for energies to log file and energy file =
97 ; Output frequency and precision for xtc file =
98 nstxout-compressed = 250
99 compressed-x-precision = 1000
100 ; This selects the subset of atoms for the xtc file. You can =
101 ; select multiple groups. By default all atoms will be written. =
102 compressed-x-grps = Protein
103 ; Selection of energy groups =
104 energygrps = Protein SOL
106 ; NEIGHBORSEARCHING PARAMETERS =
107 ; nblist update frequency =
109 ; ns algorithm (simple or grid) =
111 ; Periodic boundary conditions: xyz or none =
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 =
141 ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
142 ; Temperature coupling =
144 ; Groups to couple separately =
145 tc-grps = Protein SOL
146 ; Time constant (ps) and reference temperature (K) =
149 ; Pressure coupling =
151 Pcoupltype = Isotropic
152 ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
154 compressibility = 4.5e-5
157 ; SIMULATED ANNEALING CONTROL =
159 ; Time at which temperature should be zero (ps) =
162 ; GENERATE VELOCITIES FOR STARTUP RUN =
167 ; OPTIONS FOR BONDS =
168 constraints = all-bonds
169 ; Type of constraint algorithm =
170 constraint-algorithm = Lincs
171 ; Do not constrain the start configuration =
172 unconstrained-start = no
173 ; Relative tolerance of shake =
175 ; Highest order in the expansion of the constraint coupling matrix =
177 ; Lincs will write a warning to the stderr if in one step a bond =
178 ; rotates over more degrees than =
180 ; Convert harmonic bonds to morse potentials =
183 ; NMR refinement stuff =
184 ; Distance restraints type: No, Simple or Ensemble =
186 ; Force weighting of pairs in one distance restraint: Equal or Conservative =
187 disre-weighting = Equal
188 ; Use sqrt of the time averaged times the instantaneous violation =
192 ; Output frequency for pair distances to energy file =
195 ; Free energy control stuff =
202 ; Non-equilibrium MD stuff =
211 ; Format is number of terms (int) and for all terms an amplitude (real) =
212 ; and a phase angle (real) =
220 ; User defined thingies =