Manual:mdrun 3.3.2

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[edit] Description

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.

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.

When user-defined potential functions have been selected in the .mdp file the -table option is used to pass mdrun a formatted table with 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. When pair interactions are present a seperate table for pair interaction functions is read using the -tablep option.

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

With -multi multiple systems are simulated in parallel. As many (single node) input files are required as the number of nodes. The node number is appended to the run input and each output filename, for instance topol.tpr becomes topol0.tpr, topol1.tpr etc. The main use of this option is for NMR refinement: when distance or orientation restraints are present these can be ensemble averaged over all the systems.

With -replex replica exchange is attempted every given number of steps. This option implies -multi, see above. All run input files should use a different coupling temperature, the order of the files is not important. The random seed is set with -reseed. The velocities are scaled and neighbor searching is performed after every exchange.

Finally some experimental algorithms can be tested when the appropriate options have been given. Currently under investigation are: polarizibility, glass simulations and X-Ray bombardments.

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.


[edit] Files 

Option     Filename     Type         Description
-----------------------------------------------------
-s         topol.tpr    Input        Generic run input: tpr tpb tpa xml
-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 xml
-e         ener.edr     Output       Generic energy: edr ene
-g         md.log       Output       Log file
-dgdl      dgdl.xvg     Output, Opt. xvgr/xmgr file
-field     field.xvg    Output, Opt. xvgr/xmgr file
-table     table.xvg    Input, Opt.  xvgr/xmgr file
-tablep    tablep.xvg   Input, Opt.  xvgr/xmgr file
-rerun     rerun.xtc    Input, Opt.  Generic trajectory: xtc trr trj gro g96 pdb
-tpi       tpi.xvg      Output, Opt. xvgr/xmgr file
-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          Output, 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
-dn        dipole.ndx   Output, Opt. Index file

[edit] Options 

Option       Type   Value   Description
------------------------------------------------------
-[no]h       bool   no      Print help info and quit
-nice        int    19      Set the nicelevel
-deffnm      string         Set the default filename for all file options
-[no]xvgr    bool   yes     Add specific codes (legends etc.) in the output
                            xvg files for the xmgrace program
-np          int    1       Number of nodes, must be the same as used for
                            grompp
-nt          int    1       Number of threads to start on each node
-[no]v       bool   no      Be loud and noisy
-[no]compact bool   yes     Write a compact log file
-[no]sepdvdl bool   no      Write separate V and dVdl terms for each
                            interaction type and node to the log file(s)
-[no]multi   bool   no      Do multiple simulations in parallel (only with
                            -np > 1)
-replex      int    0       Attempt replica exchange every # steps
-reseed      int    -1      Seed for replica exchange, -1 is generate a seed
-[no]glas    bool   no      Do glass simulation with special long range
                            corrections
-[no]ionize  bool   no      Do a simulation including the effect of an X-Ray
                            bombardment on your system
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