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mdrun

mdrun

Section: GROMACS suite, VERSION 4.5 (1) Updated: Thu 26 Aug 2010
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NAME

mdrun - performs a simulation, do a normal mode analysis or an energy minimization

VERSION 4.5  

SYNOPSIS

mdrun -s topol.tpr -o traj.trr -x traj.xtc -cpi state.cpt -cpo state.cpt -c confout.gro -e ener.edr -g md.log -dhdl dhdl.xvg -field field.xvg -table table.xvg -tablep tablep.xvg -tableb table.xvg -rerun rerun.xtc -tpi tpi.xvg -tpid tpidist.xvg -ei sam.edi -eo sam.edo -j wham.gct -jo bam.gct -ffout gct.xvg -devout deviatie.xvg -runav runaver.xvg -px pullx.xvg -pf pullf.xvg -mtx nm.mtx -dn dipole.ndx -[no]h -[no]version -nice int -deffnm string -xvg enum -[no]pd -dd vector -nt int -npme int -ddorder enum -[no]ddcheck -rdd real -rcon real -dlb enum -dds real -gcom int -[no]v -[no]compact -[no]seppot -pforce real -[no]reprod -cpt real -[no]cpnum -[no]append -maxh real -multi int -replex int -reseed int -[no]ionize  

DESCRIPTION

The mdrun program is the main computational chemistry engine within GROMACS. Obviously, it performs Molecular Dynamics simulations, but it can also perform Stochastic Dynamics, Energy Minimization, test particle insertion or (re)calculation of energies. 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-minimized. 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. mdrun produces at least four output files. A single log file ( -g) is written, unless the option -seppot is used, in which case each node writes a log file. 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. Optionally coordinates can be written to a compressed trajectory file ( -x).

The option -dhdl is only used when free energy calculation is turned on.

When mdrun is started using MPI with more than 1 node, parallelization is used. By default domain decomposition is used, unless the -pd option is set, which selects particle decomposition.

With domain decomposition, the spatial decomposition can be set with option -dd. By default mdrun selects a good decomposition. The user only needs to change this when the system is very inhomogeneous. Dynamic load balancing is set with the option -dlb, which can give a significant performance improvement, especially for inhomogeneous systems. The only disadvantage of dynamic load balancing is that runs are no longer binary reproducible, but in most cases this is not important. By default the dynamic load balancing is automatically turned on when the measured performance loss due to load imbalance is 5% or more. At low parallelization these are the only important options for domain decomposition. At high parallelization the options in the next two sections could be important for increasing the performace.

When PME is used with domain decomposition, separate nodes can be assigned to do only the PME mesh calculation; this is computationally more efficient starting at about 12 nodes. The number of PME nodes is set with option -npme, this can not be more than half of the nodes. By default mdrun makes a guess for the number of PME nodes when the number of nodes is larger than 11 or performance wise not compatible with the PME grid x dimension. But the user should optimize npme. Performance statistics on this issue are written at the end of the log file. For good load balancing at high parallelization, the PME grid x and y dimensions should be divisible by the number of PME nodes (the simulation will run correctly also when this is not the case).

This section lists all options that affect the domain decomposition.

Option -rdd can be used to set the required maximum distance for inter charge-group bonded interactions. Communication for two-body bonded interactions below the non-bonded cut-off distance always comes for free with the non-bonded communication. Atoms beyond the non-bonded cut-off are only communicated when they have missing bonded interactions; this means that the extra cost is minor and nearly indepedent of the value of -rdd. With dynamic load balancing option -rdd also sets the lower limit for the domain decomposition cell sizes. By default -rdd is determined by mdrun based on the initial coordinates. The chosen value will be a balance between interaction range and communication cost.

When inter charge-group bonded interactions are beyond the bonded cut-off distance, mdrun terminates with an error message. For pair interactions and tabulated bonds that do not generate exclusions, this check can be turned off with the option -noddcheck.

When constraints are present, option -rcon influences the cell size limit as well. Atoms connected by NC constraints, where NC is the LINCS order plus 1, should not be beyond the smallest cell size. A error message is generated when this happens and the user should change the decomposition or decrease the LINCS order and increase the number of LINCS iterations. By default mdrun estimates the minimum cell size required for P-LINCS in a conservative fashion. For high parallelization it can be useful to set the distance required for P-LINCS with the option -rcon.

The -dds option sets the minimum allowed x, y and/or z scaling of the cells with dynamic load balancing. mdrun will ensure that the cells can scale down by at least this factor. This option is used for the automated spatial decomposition (when not using -dd) as well as for determining the number of grid pulses, which in turn sets the minimum allowed cell size. Under certain circumstances the value of -dds might need to be adjusted to account for high or low spatial inhomogeneity of the system.

The option -gcom can be used to only do global communication every n steps. This can improve performance for highly parallel simulations where this global communication step becomes the bottleneck. For a global thermostat and/or barostat the temperature and/or pressure will also only be updated every -gcom steps. By default it is set to the minimum of nstcalcenergy and nstlist.

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 pre-formatted 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 separate table for pair interaction functions is read using the -tablep option.

When tabulated bonded functions are present in the topology, interaction functions are read using the -tableb option. For each different tabulated interaction type the table file name is modified in a different way: before the file extension an underscore is appended, then a b for bonds, an a for angles or a d for dihedrals and finally the table number of the interaction type.

The options -px and -pf are used for writing pull COM coordinates and forces when pulling is selected in the .mdp file.

With -multi multiple systems are simulated in parallel. As many input files are required as the number of systems. The system number is appended to the run input and each output filename, for instance topol.tpr becomes topol0.tpr, topol1.tpr etc. The number of nodes per system is the total number of nodes divided by the number of systems. One 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. The number of replicas is set with the -multi option, 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: polarizability, and X-Ray bombardments.

The option -pforce is useful when you suspect a simulation crashes due to too large forces. With this option coordinates and forces of atoms with a force larger than a certain value will be printed to stderr.

Checkpoints containing the complete state of the system are written at regular intervals (option -cpt) to the file -cpo, unless option -cpt is set to -1. The previous checkpoint is backed up to state_prev.cpt to make sure that a recent state of the system is always available, even when the simulation is terminated while writing a checkpoint. With -cpnum all checkpoint files are kept and appended with the step number. A simulation can be continued by reading the full state from file with option -cpi. This option is intelligent in the way that if no checkpoint file is found, Gromacs just assumes a normal run and starts from the first step of the tpr file. By default the output will be appending to the existing output files. The checkpoint file contains checksums of all output files, such that you will never loose data when some output files are modified, corrupt or removed. There are three scenarios with -cpi:

* no files with matching names are present: new output files are written

* all files are present with names and checksums matching those stored in the checkpoint file: files are appended

* otherwise no files are modified and a fatal error is generated

With -noappend new output files are opened and the simulation part number is added to all output file names. Note that in all cases the checkpoint file itself is not renamed and will be overwritten, unless its name does not match the -cpo option.

With checkpointing the output is appended to previously written output files, unless -noappend is used or none of the previous output files are present (except for the checkpoint file). The integrity of the files to be appended is verified using checksums which are stored in the checkpoint file. This ensures that output can not be mixed up or corrupted due to file appending. When only some of the previous output files are present, a fatal error is generated and no old output files are modified and no new output files are opened. The result with appending will be the same as from a single run. The contents will be binary identical, unless you use a different number of nodes or dynamic load balancing or the FFT library uses optimizations through timing.

With option -maxh a simulation is terminated and a checkpoint file is written at the first neighbor search step where the run time exceeds -maxh*0.99 hours.

When mdrun receives a TERM signal, it will set nsteps to the current step plus one. When mdrun receives an INT signal (e.g. when ctrl+C is pressed), it will stop after the next neighbor search step (with nstlist=0 at the next 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.

When mdrun is started with MPI, it does not run niced by default.  

FILES

-s topol.tpr Input
 Run input file: tpr tpb tpa 

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

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

-cpi state.cpt Input, Opt.
 Checkpoint file 

-cpo state.cpt Output, Opt.
 Checkpoint file 

-c confout.gro Output
 Structure file: gro g96 pdb etc. 

-e ener.edr Output
 Energy file 

-g md.log Output
 Log file 

-dhdl dhdl.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 

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

-rerun rerun.xtc Input, Opt.
 Trajectory: xtc trr trj gro g96 pdb cpt 

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

-tpid tpidist.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 

-px pullx.xvg Output, Opt.
 xvgr/xmgr file 

-pf pullf.xvg Output, Opt.
 xvgr/xmgr file 

-mtx nm.mtx Output, Opt.
 Hessian matrix 

-dn dipole.ndx Output, Opt.
 Index file 

 

OTHER OPTIONS

-[no]hno
 Print help info and quit

-[no]versionno
 Print version info and quit

-nice int 0
 Set the nicelevel

-deffnm string
 Set the default filename for all file options

-xvg enum xmgrace
 xvg plot formatting:  xmgrace xmgr or  none

-[no]pdno
 Use particle decompostion

-dd vector 0 0 0
 Domain decomposition grid, 0 is optimize

-nt int 0
 Number of threads to start (0 is guess)

-npme int -1
 Number of separate nodes to be used for PME, -1 is guess

-ddorder enum interleave
 DD node order:  interleave pp_pme or  cartesian

-[no]ddcheckyes
 Check for all bonded interactions with DD

-rdd real 0
 The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates

-rcon real 0
 Maximum distance for P-LINCS (nm), 0 is estimate

-dlb enum auto
 Dynamic load balancing (with DD):  auto no or  yes

-dds real 0.8
 Minimum allowed dlb scaling of the DD cell size

-gcom int -1
 Global communication frequency

-[no]vno
 Be loud and noisy

-[no]compactyes
 Write a compact log file

-[no]seppotno
 Write separate V and dVdl terms for each interaction type and node to the log file(s)

-pforce real -1
 Print all forces larger than this (kJ/mol nm)

-[no]reprodno
 Try to avoid optimizations that affect binary reproducibility

-cpt real 15
 Checkpoint interval (minutes)

-[no]cpnumno
 Keep and number checkpoint files

-[no]appendyes
 Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names

-maxh real -1
 Terminate after 0.99 times this time (hours)

-multi int 0
 Do multiple simulations in parallel

-replex int 0
 Attempt replica exchange every  steps

-reseed int -1
 Seed for replica exchange, -1 is generate a seed

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

 

SEE ALSO

gromacs(7)

More information about GROMACS is available at <http://www.gromacs.org/>.


 

Index

NAME
SYNOPSIS
DESCRIPTION
FILES
OTHER OPTIONS
SEE ALSO

This document was created by man2html, using the manual pages.
Time: 21:23:49 GMT, April 16, 2011