.TH mdrun 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME mdrun - performs a simulation, do a normal mode analysis or an energy minimization .B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3mdrun\fP .BI "\-s" " topol.tpr " .BI "\-o" " traj.trr " .BI "\-x" " traj.xtc " .BI "\-cpi" " state.cpt " .BI "\-cpo" " state.cpt " .BI "\-c" " confout.gro " .BI "\-e" " ener.edr " .BI "\-g" " md.log " .BI "\-dhdl" " dhdl.xvg " .BI "\-field" " field.xvg " .BI "\-table" " table.xvg " .BI "\-tablep" " tablep.xvg " .BI "\-tableb" " table.xvg " .BI "\-rerun" " rerun.xtc " .BI "\-tpi" " tpi.xvg " .BI "\-tpid" " tpidist.xvg " .BI "\-ei" " sam.edi " .BI "\-eo" " sam.edo " .BI "\-j" " wham.gct " .BI "\-jo" " bam.gct " .BI "\-ffout" " gct.xvg " .BI "\-devout" " deviatie.xvg " .BI "\-runav" " runaver.xvg " .BI "\-px" " pullx.xvg " .BI "\-pf" " pullf.xvg " .BI "\-mtx" " nm.mtx " .BI "\-dn" " dipole.ndx " .BI "\-multidir" " rundir " .BI "\-[no]h" "" .BI "\-[no]version" "" .BI "\-nice" " int " .BI "\-deffnm" " string " .BI "\-xvg" " enum " .BI "\-[no]pd" "" .BI "\-dd" " vector " .BI "\-npme" " int " .BI "\-ddorder" " enum " .BI "\-[no]ddcheck" "" .BI "\-rdd" " real " .BI "\-rcon" " real " .BI "\-dlb" " enum " .BI "\-dds" " real " .BI "\-gcom" " int " .BI "\-[no]v" "" .BI "\-[no]compact" "" .BI "\-[no]seppot" "" .BI "\-pforce" " real " .BI "\-[no]reprod" "" .BI "\-cpt" " real " .BI "\-[no]cpnum" "" .BI "\-[no]append" "" .BI "\-maxh" " real " .BI "\-multi" " int " .BI "\-replex" " int " .BI "\-reseed" " int " .BI "\-[no]ionize" "" .SH DESCRIPTION \&The \fB mdrun\fR 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 \fB mdrun\fR \&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 \fB g_nmeig\fR. \&The \fB mdrun\fR program reads the run input file (\fB \-s\fR) \&and distributes the topology over nodes if needed. \&\fB mdrun\fR produces at least four output files. \&A single log file (\fB \-g\fR) is written, unless the option \&\fB \-seppot\fR is used, in which case each node writes a log file. \&The trajectory file (\fB \-o\fR), contains coordinates, velocities and \&optionally forces. \&The structure file (\fB \-c\fR) contains the coordinates and \&velocities of the last step. \&The energy file (\fB \-e\fR) 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 \&(\fB \-x\fR). \&The option \fB \-dhdl\fR is only used when free energy calculation is \&turned on. \&When \fB mdrun\fR is started using MPI with more than 1 node, parallelization \&is used. By default domain decomposition is used, unless the \fB \-pd\fR \&option is set, which selects particle decomposition. \&With domain decomposition, the spatial decomposition can be set \&with option \fB \-dd\fR. By default \fB mdrun\fR 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 \fB \-dlb\fR, \&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 \fB \-npme\fR, \&this can not be more than half of the nodes. \&By default \fB mdrun\fR makes a guess for the number of PME \&nodes when the number of nodes is larger than 11 or performance wise \¬ 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 \fB \-rdd\fR 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 \fB \-rdd\fR. \&With dynamic load balancing option \fB \-rdd\fR also sets \&the lower limit for the domain decomposition cell sizes. \&By default \fB \-rdd\fR is determined by \fB mdrun\fR 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, \fB mdrun\fR 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 \fB \-noddcheck\fR. \& \&When constraints are present, option \fB \-rcon\fR 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 \fB mdrun\fR 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 \fB \-rcon\fR. \& \&The \fB \-dds\fR option sets the minimum allowed x, y and/or z scaling \&of the cells with dynamic load balancing. \fB mdrun\fR 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 \fB \-dd\fR) \&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 \fB \-dds\fR might need to be adjusted to account for \&high or low spatial inhomogeneity of the system. \& \&The option \fB \-gcom\fR 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 \fB \-gcom\fR steps. \&By default it is set to the minimum of nstcalcenergy and nstlist. \&With \fB \-rerun\fR an input trajectory can be given for which \&forces and energies will be (re)calculated. Neighbor searching will be \&performed for every frame, unless \fB nstlist\fR is zero \&(see the \fB .mdp\fR file). \&ED (essential dynamics) sampling is switched on by using the \fB \-ei\fR \&flag followed by an \fB .edi\fR file. \&The \fB .edi\fR file can be produced using options in the essdyn \&menu of the WHAT IF program. \fB mdrun\fR produces a \fB .edo\fR file that \&contains projections of positions, velocities and forces onto selected \&eigenvectors. \&When user\-defined potential functions have been selected in the \&\fB .mdp\fR file the \fB \-table\fR option is used to pass \fB mdrun\fR \&a formatted table with potential functions. The file is read from \&either the current directory or from the \fB GMXLIB\fR directory. \&A number of pre\-formatted tables are presented in the \fB GMXLIB\fR 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 \fB \-tablep\fR option. \&When tabulated bonded functions are present in the topology, \&interaction functions are read using the \fB \-tableb\fR 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 \fB \-px\fR and \fB \-pf\fR are used for writing pull COM \&coordinates and forces when pulling is selected \&in the \fB .mdp\fR file. \&With \fB \-multi\fR or \fB \-multidir\fR, multiple systems can be \&simulated in parallel. \&As many input files/directories are required as the number of systems. \&The \fB \-multidir\fR option takes a list of directories (one for each \&system) and runs in each of them, using the input/output file names, \&such as specified by e.g. the \fB \-s\fR option, relative to these \&directories. \&With \fB \-multi\fR, the system number is appended to the run input \&and each output filename, for instance \fB topol.tpr\fR becomes \&\fB topol0.tpr\fR, \fB topol1.tpr\fR etc. \&The number of nodes per system is the total number of nodes \÷d 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 \fB \-replex\fR replica exchange is attempted every given number \&of steps. The number of replicas is set with the \fB \-multi\fR or \&\fB \-multidir\fR option, described 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 \&\fB \-reseed\fR. 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 \fB \-pforce\fR 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 \fB \-cpt\fR) to the file \fB \-cpo\fR, \&unless option \fB \-cpt\fR is set to \-1. \&The previous checkpoint is backed up to \fB state_prev.cpt\fR to \&make sure that a recent state of the system is always available, \&even when the simulation is terminated while writing a checkpoint. \&With \fB \-cpnum\fR 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 \fB \-cpi\fR. 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 \fB .tpr\fR 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 \fB \-cpi\fR: \&\fB *\fR no files with matching names are present: new output files are written \&\fB *\fR all files are present with names and checksums matching those stored \&in the checkpoint file: files are appended \&\fB *\fR otherwise no files are modified and a fatal error is generated \&With \fB \-noappend\fR 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 \fB \-cpo\fR option. \& \&With checkpointing the output is appended to previously written \&output files, unless \fB \-noappend\fR 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 \¬ 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 \fB \-maxh\fR a simulation is terminated and a checkpoint \&file is written at the first neighbor search step where the run time \&exceeds \fB \-maxh\fR*0.99 hours. \& \&When \fB mdrun\fR receives a TERM signal, it will set nsteps to the current \&step plus one. When \fB mdrun\fR 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 \fB mdrun\fR processes \&is sufficient, this signal should not be sent to mpirun or \&the \fB mdrun\fR process that is the parent of the others. \& \&When \fB mdrun\fR is started with MPI, it does not run niced by default. .SH FILES .BI "\-s" " topol.tpr" .B Input Run input file: tpr tpb tpa .BI "\-o" " traj.trr" .B Output Full precision trajectory: trr trj cpt .BI "\-x" " traj.xtc" .B Output, Opt. Compressed trajectory (portable xdr format) .BI "\-cpi" " state.cpt" .B Input, Opt. Checkpoint file .BI "\-cpo" " state.cpt" .B Output, Opt. Checkpoint file .BI "\-c" " confout.gro" .B Output Structure file: gro g96 pdb etc. .BI "\-e" " ener.edr" .B Output Energy file .BI "\-g" " md.log" .B Output Log file .BI "\-dhdl" " dhdl.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-field" " field.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-table" " table.xvg" .B Input, Opt. xvgr/xmgr file .BI "\-tablep" " tablep.xvg" .B Input, Opt. xvgr/xmgr file .BI "\-tableb" " table.xvg" .B Input, Opt. xvgr/xmgr file .BI "\-rerun" " rerun.xtc" .B Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt .BI "\-tpi" " tpi.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-tpid" " tpidist.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-ei" " sam.edi" .B Input, Opt. ED sampling input .BI "\-eo" " sam.edo" .B Output, Opt. ED sampling output .BI "\-j" " wham.gct" .B Input, Opt. General coupling stuff .BI "\-jo" " bam.gct" .B Output, Opt. General coupling stuff .BI "\-ffout" " gct.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-devout" " deviatie.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-runav" " runaver.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-px" " pullx.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-pf" " pullf.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-mtx" " nm.mtx" .B Output, Opt. Hessian matrix .BI "\-dn" " dipole.ndx" .B Output, Opt. Index file .BI "\-multidir" " rundir" .B Input, Opt., Mult. Run directory .SH OTHER OPTIONS .BI "\-[no]h" "no " Print help info and quit .BI "\-[no]version" "no " Print version info and quit .BI "\-nice" " int" " 0" Set the nicelevel .BI "\-deffnm" " string" " " Set the default filename for all file options .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR .BI "\-[no]pd" "no " Use particle decompostion .BI "\-dd" " vector" " 0 0 0" Domain decomposition grid, 0 is optimize .BI "\-npme" " int" " \-1" Number of separate nodes to be used for PME, \-1 is guess .BI "\-ddorder" " enum" " interleave" DD node order: \fB interleave\fR, \fB pp_pme\fR or \fB cartesian\fR .BI "\-[no]ddcheck" "yes " Check for all bonded interactions with DD .BI "\-rdd" " real" " 0 " The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates .BI "\-rcon" " real" " 0 " Maximum distance for P\-LINCS (nm), 0 is estimate .BI "\-dlb" " enum" " auto" Dynamic load balancing (with DD): \fB auto\fR, \fB no\fR or \fB yes\fR .BI "\-dds" " real" " 0.8 " Minimum allowed dlb scaling of the DD cell size .BI "\-gcom" " int" " \-1" Global communication frequency .BI "\-[no]v" "no " Be loud and noisy .BI "\-[no]compact" "yes " Write a compact log file .BI "\-[no]seppot" "no " Write separate V and dVdl terms for each interaction type and node to the log file(s) .BI "\-pforce" " real" " \-1 " Print all forces larger than this (kJ/mol nm) .BI "\-[no]reprod" "no " Try to avoid optimizations that affect binary reproducibility .BI "\-cpt" " real" " 15 " Checkpoint interval (minutes) .BI "\-[no]cpnum" "no " Keep and number checkpoint files .BI "\-[no]append" "yes " Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names .BI "\-maxh" " real" " \-1 " Terminate after 0.99 times this time (hours) .BI "\-multi" " int" " 0" Do multiple simulations in parallel .BI "\-replex" " int" " 0" Attempt replica exchange every steps .BI "\-reseed" " int" " \-1" Seed for replica exchange, \-1 is generate a seed .BI "\-[no]ionize" "no " Do a simulation including the effect of an X\-Ray bombardment on your system .SH SEE ALSO .BR gromacs(7) More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.