--- name: "mdrun_mpi.openmpi" section: "1" platform: "linux" package: "gromacs-openmpi" version: "2020.6-2" release: "Debian 11 (Bullseye)" platforms: ["linux"] url: "https://new.carta.tech/mdrun_mpi.openmpi" --- # mdrun\_mpi.openmpi(1) Perform a simulation, do a normal mode analysis or an energy minimization ## NAME mdrun\_mpi - Perform a simulation, do a normal mode analysis or an energy minimization ## SYNOPSIS ``` mdrun_mpi [-s [<.tpr>]] [-cpi [<.cpt>]] [-table [<.xvg>]] [-tablep [<.xvg>]] [-tableb [<.xvg> [...]]] [-rerun [<.xtc/.trr/...>]] [-ei [<.edi>]] [-multidir [ [...]]] [-awh [<.xvg>]] [-membed [<.dat>]] [-mp [<.top>]] [-mn [<.ndx>]] [-o [<.trr/.cpt/...>]] [-x [<.xtc/.tng>]] [-cpo [<.cpt>]] [-c [<.gro/.g96/...>]] [-e [<.edr>]] [-g [<.log>]] [-dhdl [<.xvg>]] [-field [<.xvg>]] [-tpi [<.xvg>]] [-tpid [<.xvg>]] [-eo [<.xvg>]] [-px [<.xvg>]] [-pf [<.xvg>]] [-ro [<.xvg>]] [-ra [<.log>]] [-rs [<.log>]] [-rt [<.log>]] [-mtx [<.mtx>]] [-if [<.xvg>]] [-swap [<.xvg>]] [-deffnm ] [-xvg ] [-dd ] [-ddorder ] [-npme ] [-nt ] [-ntmpi ] [-ntomp ] [-ntomp_pme ] [-pin ] [-pinoffset ] [-pinstride ] [-gpu_id ] [-gputasks ] [-[no]ddcheck] [-rdd ] [-rcon ] [-dlb ] [-dds ] [-nb ] [-nstlist ] [-[no]tunepme] [-pme ] [-pmefft ] [-bonded ] [-update ] [-[no]v] [-pforce ] [-[no]reprod] [-cpt ] [-[no]cpnum] [-[no]append] [-nsteps ] [-maxh ] [-replex ] [-nex ] [-reseed ] ``` ## DESCRIPTION **mdrun\_mpi** *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 gmx nmeig.* *The* **mdrun** *program reads the run input file (***-s***)* *and distributes the topology over ranks if needed.* **mdrun** *produces at least four output files.* *A single log file (***-g***) is written.* *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.* *Running mdrun efficiently in parallel is a complex topic,* *many aspects of which are covered in the online User Guide. You* *should look there for practical advice on using many of the options* *available in mdrun.* *ED (essential dynamics) sampling and/or additional flooding potentials* *are switched on by using the* **-ei** *flag followed by an .edi* *file. The .edi file can be produced with the* **make\_edi** *tool* *or by using options in the essdyn menu of the WHAT IF program.* **mdrun** *produces a .xvg output 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 used, a table file name must* *be given. For the topology to work, a file name given here must match a* *character sequence before the file extension. That sequence is: an underscore,* *then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals,* *and finally the matching table number index used in the topology. Note that,* *these options are deprecated, and in future will be available via grompp.* *The options* **-px** *and* **-pf** *are used for writing pull COM* *coordinates and forces when pulling is selected* *in the .mdp file.* *The option* **-membed** *does what used to be g\_membed, i.e. embed* *a protein into a membrane. This module requires a number of settings* *that are provided in a data file that is the argument of this option.* *For more details in membrane embedding, see the documentation in the* *user guide. The options* **-mn** *and* **-mp** *are used to provide* *the index and topology files used for the embedding.* *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. It will also terminate the run when non-finite* *forces are present.* *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 ranks 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. This option is particularly useful in* *combination with setting* **nsteps** *to -1 either in the mdp or using the* *similarly named command line option (although the latter is deprecated).* *This results in an infinite run,* *terminated only when the time limit set by* **-maxh** *is reached (if any)* *or upon receiving a signal.* *Interactive molecular dynamics (IMD) can be activated by using at least one* *of the three IMD switches: The* **-imdterm** *switch allows one to terminate* *the simulation from the molecular viewer (e.g. VMD). With* **-imdwait***,* **mdrun** *pauses whenever no IMD client is connected. Pulling from the* *IMD remote can be turned on by* **-imdpull***.* *The port* **mdrun** *listens to can be altered by* **-imdport***.The* *file pointed to by* **-if** *contains atom indices and forces if IMD* *pulling is used.* ## OPTIONS *Options to specify input files:* - **-s \[\<.tpr\>\] (topol.tpr)** *Portable xdr run input file* - **-cpi \[\<.cpt\>\] (state.cpt) (Optional)** *Checkpoint file* - **-table \[\<.xvg\>\] (table.xvg) (Optional)** *xvgr/xmgr file* - **-tablep \[\<.xvg\>\] (tablep.xvg) (Optional)** *xvgr/xmgr file* - **-tableb \[\<.xvg\> \[...\]\] (table.xvg) (Optional)** *xvgr/xmgr file* - **-rerun \[\<.xtc/.trr/...\>\] (rerun.xtc) (Optional)** *Trajectory: xtc trr cpt gro g96 pdb tng* - **-ei \[\<.edi\>\] (sam.edi) (Optional)** *ED sampling input* - **-multidir \[\ \[...\]\] (rundir) (Optional)** *Run directory* - **-awh \[\<.xvg\>\] (awhinit.xvg) (Optional)** *xvgr/xmgr file* - **-membed \[\<.dat\>\] (membed.dat) (Optional)** *Generic data file* - **-mp \[\<.top\>\] (membed.top) (Optional)** *Topology file* - **-mn \[\<.ndx\>\] (membed.ndx) (Optional)** *Index file* *Options to specify output files:* - **-o \[\<.trr/.cpt/...\>\] (traj.trr)** *Full precision trajectory: trr cpt tng* - **-x \[\<.xtc/.tng\>\] (traj\_comp.xtc) (Optional)** *Compressed trajectory (tng format or portable xdr format)* - **-cpo \[\<.cpt\>\] (state.cpt) (Optional)** *Checkpoint file* - **-c \[\<.gro/.g96/...\>\] (confout.gro)** *Structure file: gro g96 pdb brk ent esp* - **-e \[\<.edr\>\] (ener.edr)** *Energy file* - **-g \[\<.log\>\] (md.log)** *Log file* - **-dhdl \[\<.xvg\>\] (dhdl.xvg) (Optional)** *xvgr/xmgr file* - **-field \[\<.xvg\>\] (field.xvg) (Optional)** *xvgr/xmgr file* - **-tpi \[\<.xvg\>\] (tpi.xvg) (Optional)** *xvgr/xmgr file* - **-tpid \[\<.xvg\>\] (tpidist.xvg) (Optional)** *xvgr/xmgr file* - **-eo \[\<.xvg\>\] (edsam.xvg) (Optional)** *xvgr/xmgr file* - **-px \[\<.xvg\>\] (pullx.xvg) (Optional)** *xvgr/xmgr file* - **-pf \[\<.xvg\>\] (pullf.xvg) (Optional)** *xvgr/xmgr file* - **-ro \[\<.xvg\>\] (rotation.xvg) (Optional)** *xvgr/xmgr file* - **-ra \[\<.log\>\] (rotangles.log) (Optional)** *Log file* - **-rs \[\<.log\>\] (rotslabs.log) (Optional)** *Log file* - **-rt \[\<.log\>\] (rottorque.log) (Optional)** *Log file* - **-mtx \[\<.mtx\>\] (nm.mtx) (Optional)** *Hessian matrix* - **-if \[\<.xvg\>\] (imdforces.xvg) (Optional)** *xvgr/xmgr file* - **-swap \[\<.xvg\>\] (swapions.xvg) (Optional)** *xvgr/xmgr file* *Other options:* - **-deffnm \** *Set the default filename for all file options* - **-xvg \ (xmgrace)** *xvg plot formatting: xmgrace, xmgr, none* - **-dd \ (0 0 0)** *Domain decomposition grid, 0 is optimize* - **-ddorder \ (interleave)** *DD rank order: interleave, pp\_pme, cartesian* - **-npme \ (-1)** *Number of separate ranks to be used for PME, -1 is guess* - **-nt \ (0)** *Total number of threads to start (0 is guess)* - **-ntmpi \ (0)** *Number of thread-MPI ranks to start (0 is guess)* - **-ntomp \ (0)** *Number of OpenMP threads per MPI rank to start (0 is guess)* - **-ntomp\_pme \ (0)** *Number of OpenMP threads per MPI rank to start (0 is -ntomp)* - **-pin \ (auto)** *Whether mdrun should try to set thread affinities: auto, on, off* - **-pinoffset \ (0)** *The lowest logical core number to which mdrun should pin the first thread* - **-pinstride \ (0)** *Pinning distance in logical cores for threads, use 0 to minimize the number of threads per physical core* - **-gpu\_id \** *List of unique GPU device IDs available to use* - **-gputasks \** *List of GPU device IDs, mapping each PP task on each node to a device* - **-\[no\]ddcheck (yes)** *Check for all bonded interactions with DD* - **-rdd \ (0)** *The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates* - **-rcon \ (0)** *Maximum distance for P-LINCS (nm), 0 is estimate* - **-dlb \ (auto)** *Dynamic load balancing (with DD): auto, no, yes* - **-dds \ (0.8)** *Fraction in (0,1) by whose reciprocal the initial DD cell size will be increased in order to provide a margin in which dynamic load balancing can act while preserving the minimum cell size.* - **-nb \ (auto)** *Calculate non-bonded interactions on: auto, cpu, gpu* - **-nstlist \ (0)** *Set nstlist when using a Verlet buffer tolerance (0 is guess)* - **-\[no\]tunepme (yes)** *Optimize PME load between PP/PME ranks or GPU/CPU* - **-pme \ (auto)** *Perform PME calculations on: auto, cpu, gpu* - **-pmefft \ (auto)** *Perform PME FFT calculations on: auto, cpu, gpu* - **-bonded \ (auto)** *Perform bonded calculations on: auto, cpu, gpu* - **-update \ (auto)** *Perform update and constraints on: auto, cpu, gpu* - **-\[no\]v (no)** *Be loud and noisy* - **-pforce \ (-1)** *Print all forces larger than this (kJ/mol nm)* - **-\[no\]reprod (no)** *Try to avoid optimizations that affect binary reproducibility* - **-cpt \ (15)** *Checkpoint interval (minutes)* - **-\[no\]cpnum (no)** *Keep and number checkpoint files* - **-\[no\]append (yes)** *Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names* - **-nsteps \ (-2)** *Run this number of steps (-1 means infinite, -2 means use mdp option, smaller is invalid)* - **-maxh \ (-1)** *Terminate after 0.99 times this time (hours)* - **-replex \ (0)** *Attempt replica exchange periodically with this period (steps)* - **-nex \ (0)** *Number of random exchanges to carry out each exchange interval (N^3 is one suggestion). -nex zero or not specified gives neighbor replica exchange.* - **-reseed \ (-1)** *Seed for replica exchange, -1 is generate a seed* ## SEE ALSO **[gmx(1)](/gmx/1.md)** *More information about GROMACS is available at \.* ## COPYRIGHT *2020, GROMACS development team*