mdrun_mpi VERSION 3.1

mdrun_mpi -s topol.tpr -o traj.trr -x traj.xtc -c confout.gro -e ener.edr -g md.log -dgdl dgdl.xvg -table table.xvg -rerun rerun.xtc -ei sam.edi -eo sam.edo -j wham.gct -jo bam.gct -ffout gct.xvg -devout deviatie.xvg -runav runaver.xvg -pi pull.ppa -po pullout.ppa -pd pull.pdo -pn pull.ndx -mtx nm.mtx -[no]h -[no]X -nice int -deffnm string -np int -[no]v -[no]compact -[no]multi -[no]glas -[no]ionize

The mdrun program is the main computational chemistry engine within GROMACS. Obviously, it performs Molecular Dynamics simulations, but it can also perform Brownian Dynamics and Langevin Dynamics as well as Conjugate Gradient or Steepest Descents energy minimization. Normal mode analysis is another option. In this case mdrun builds a Hessian matrix from single conformation. For usual Normal Modes-like calculations, make sure that the structure provided is properly energy-minimised. The generated matrix can be diagonalized by g_nmeig.

This version of the program will only run while using the LAM-MPI parallel computing library. See lamboot(1) and mpirun(1). Use the normal mdrun(1) program for conventional single-threaded operations.

The mdrun program reads the run input file ( -s ) and distributes the topology over nodes if needed. The coordinates are passed around, so that computations can begin. First a neighborlist is made, then the forces are computed. The forces are globally summed, and the velocities and positions are updated. If necessary shake is performed to constrain bond lengths and/or bond angles. Temperature and Pressure can be controlled using weak coupling to a bath.

mdrun produces at least three output file, plus one log file ( -g ) per node. The trajectory file ( -o ), contains coordinates, velocities and optionally forces. The structure file ( -c ) contains the coordinates and velocities of the last step. The energy file ( -e ) contains energies, the temperature, pressure, etc, a lot of these things are also printed in the log file of node 0. Optionally coordinates can be written to a compressed trajectory file ( -x ).

When running in parallel with PVM or an old version of MPI the

-np option must be given to indicate the number of nodes.

The option -dgdl is only used when free energy perturbation is turned on.

With -rerun an input trajectory can be given for which forces and energies will be (re)calculated. Neighbor searching will be performed for every frame, unless nstlist is zero (see the .mdp file).

ED (essential dynamics) sampling is switched on by using the -ei

flag followed by an .edi file. The .edi file can be produced using options in the essdyn menu of the WHAT IF program. mdrun produces a .edo file that contains projections of positions, velocities and forces onto selected eigenvectors.

The -table option can be used to pass mdrun a formatted table with user-defined potential functions. The file is read from either the current directory or from the GMXLIB directory. A number of preformatted tables are presented in the GMXLIB dir, for 6-8, 6-9, 6-10, 6-11, 6-12 Lennard Jones potentials with normal Coulomb.

The options -pi , -po , -pd , -pn are used for potential of mean force calculations and umbrella sampling. See manual.

When mdrun receives a TERM signal, it will set nsteps to the current step plus one. When mdrun receives a USR1 signal, it will set nsteps to the next multiple of nstxout after the current step. In both cases all the usual output will be written to file. When running with MPI, a signal to one of the mdrun processes is sufficient, this signal should not be sent to mpirun or the mdrun process that is the parent of the others. Finally some experimental algorithms can be tested when the appropriate options have been given. Currently under investigation are: polarizibility, glass simulations, Free energy perturbation, X-Ray bombardments and parallel independent simulations.

-s topol.tpr Input Generic run input: tpr tpb tpa

-o traj.trr Output Full precision trajectory: trr trj

-x traj.xtc Output, Opt. Compressed trajectory (portable xdr format)

-c confout.gro Output Generic structure: gro g96 pdb

-e ener.edr Output Generic energy: edr ene

-g md.log Output Log file

-dgdl dgdl.xvg Output, Opt. xvgr/xmgr file

-table table.xvg Input, Opt. xvgr/xmgr file

-rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb

-ei sam.edi Input, Opt. ED sampling input

-eo sam.edo Output, Opt. ED sampling output

-j wham.gct Input, Opt. General coupling stuff

-jo bam.gct Input, Opt. General coupling stuff

-ffout gct.xvg Output, Opt. xvgr/xmgr file

-devout deviatie.xvg Output, Opt. xvgr/xmgr file

-runav runaver.xvg Output, Opt. xvgr/xmgr file

-pi pull.ppa Input, Opt. Pull parameters

-po pullout.ppa Output, Opt. Pull parameters

-pd pull.pdo Output, Opt. Pull data output

-pn pull.ndx Input, Opt. Index file

-mtx nm.mtx Output, Opt. Hessian matrix

-[no]h no Print help info and quit

-[no]X no Use dialog box GUI to edit command line options

-nice int 19 Set the nicelevel

-deffnm string Set the default filename for all file options

-np int 1 Number of nodes, must be the same as used for grompp

-[no]v no Be loud and noisy

-[no]compact yes Write a compact log file

-[no]multi no Do multiple simulations in parallel (only with -np 1)

-[no]glas no Do glass simulation with special long range corrections

-[no]ionize no Do a simulation including the effect of an X-Ray bombardment on your system