mdp options Main Table of Contents

VERSION 3.1 Wed 27 Feb 2002

Table of Contents

• General remarks

• preprocessing (title, warnings, cpp, include, define)
• run control (integrator, tinit, dt, nsteps, comm_mode, nstcomm, comm_grps)
• langevin dynamics (bd_temp, bd_fric, ld_seed)
• energy minimization (emtol, emstep, nstcgsteep)
• shell molecular dynamics(emtol,niter)
• output control (nstxout, nstvout, nstfout, nstlog, nstenergy, nstxtcout, xtc_precision, xtc_grps, energygrps)
• neighbor searching (nstlist, ns_type, pbc, rlist)
• electrostatics and VdW (coulombtype, rcoulomb_switch, rcoulomb, vdwtype, rvdw_switch, rvdw, epsilon_r, DispCorr, fourierspacing, fourier_nx, fourier_ny, fourier_nz, pme_order, ewald_rtol, ewald_geometry, surface_epsilon, optimize_fft)
• Temperature coupling (tcoupl, tc_grps, tau_t, ref_t)
• Pressure coupling (pcoupl, pcoupltype, tau_p, compressibility, ref_p)
• simulated annealing (annealing, zero_temp_time)
• velocity generation (gen_vel, gen_temp, gen_seed)
• bonds (constraints, constraint_algorithm, unconstrained_start, shake_tol, lincs_order, lincs_warnangle, morse)
• Energy group exclusions (energygrp_excl)
• NMR refinement (disre, disre_weighting, disre_mixed, disre_fc, disre_tau, nstdisreout, orire, orire_fc, orire_tau, orire_fitgrp, nstorireout)
• Free Energy Perturbation (free_energy, init_lambda, delta_lambda, sc_alpha, sc_sigma)
• Non-equilibrium MD (acc_grps, accelerate, freezegrps, freezedim, cos_acceleration)
• Electric fields (E_x, E_xt, E_y, E_yt, E_z, E_zt )
• User defined thingies (user1_grps, user2_grps, userint1, userint2, userint3, userint4, userreal1, userreal2, userreal3, userreal4)
• Index

A sample .mdp file is available. This should be appropriate to start a normal simulation. Edit it to suit your specific needs and desires.

title:

this is redundant, so you can type anything you want

cpp: (/lib/cpp)

your preprocessor

include:

directories to include in your topology. Format:

-I/home/john/my_lib -I../more_lib

define: ()

defines to pass to the preprocessor, default is no defines. You can use any defines to control options in your customized topology files. Options that are already available by default are:

-DFLEX_SPC

Will tell grompp to include FLEX_SPC in stead of SPC into your topology, this is necessary to make conjugate gradient work and will allow steepest descent to minimize further.

-DPOSRE

Will tell grompp to include posre.itp into your topology, used for position restraints.

integrator:

md

A leap-frog algorithm for integrating Newton's equations of motion.

sd

A leap-frog stochastic dynamics integrator. The temperature for one or more groups of atoms (tc_grps) is set with ref_t [K], the inverse friction constant for each group is set with tau_t [ps]. The parameter tcoupl is ignored. The random generator is initialized with ld_seed.
NOTE: temperature deviations decay twice as fast as with a Berendsen thermostat with the same tau_t.

bd

An Euler integrator for Brownian or position Langevin dynamics, the velocity is the force divided by a friction coefficient (bd_fric [amu ps^-1]) plus random thermal noise (bd_temp [K]). When bd_fric=0, the friction coefficient for each particle is calculated as mass/tau_t, as for the integrator sd. The random generator is initialized with ld_seed.

The following algorithms are not integrators, but selected using the integrator tag anyway

steep

A steepest descent algorithm for energy minimization. The maximum step size is emstep [nm], the tolerance is emtol [kJ mol^-1 nm^-1].

cg

A conjugate gradient algorithm for energy minimization, the tolerance is emtol [kJ mol^-1 nm^-1]. CG is more efficient when a steepest descent step is done every once in a while, this is determined by nstcgsteep. For a minimization prior to a normal mode analysis, which requires a very high accuracy, GROMACS should be compiled in double precision.

nm

Normal mode analysis is performed on the structure in the tpr file

. GROMACS should be compiled in double precision.

bd_temp: (300) [K]

temperature in Brownian dynamics run (controls thermal noise level). When bd_fric=0, ref_t is used instead.

bd_fric: (0) [amu ps^-1]

Brownian dynamics friction coefficient. When bd_fric=0, the friction coefficient for each particle is calculated as mass/tau_t.