xenial (1) mdrun_mpi.openmpi.1.gz

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NAME

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

SYNOPSIS

          gmx mdrun [-s [<.tpr>]] [-cpi [<.cpt>]] [-table [<.xvg>]]
                    [-tabletf [<.xvg>]] [-tablep [<.xvg>]] [-tableb [<.xvg>]]
                    [-rerun [<.xtc/.trr/...>]] [-ei [<.edi>]]
                    [-multidir [<dir> [...]]] [-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>]]
                    [-devout [<.xvg>]] [-runav [<.xvg>]] [-px [<.xvg>]]
                    [-pf [<.xvg>]] [-ro [<.xvg>]] [-ra [<.log>]] [-rs [<.log>]]
                    [-rt [<.log>]] [-mtx [<.mtx>]] [-dn [<.ndx>]]
                    [-if [<.xvg>]] [-swap [<.xvg>]] [-deffnm <string>]
                    [-xvg <enum>] [-dd <vector>] [-ddorder <enum>]
                    [-npme <int>] [-nt <int>] [-ntmpi <int>] [-ntomp <int>]
                    [-ntomp_pme <int>] [-pin <enum>] [-pinoffset <int>]
                    [-pinstride <int>] [-gpu_id <string>] [-[no]ddcheck]
                    [-rdd <real>] [-rcon <real>] [-dlb <enum>] [-dds <real>]
                    [-gcom <int>] [-nb <enum>] [-nstlist <int>] [-[no]tunepme]
                    [-[no]v] [-[no]compact] [-pforce <real>] [-[no]reprod]
                    [-cpt <real>] [-[no]cpnum] [-[no]append] [-nsteps <int>]
                    [-maxh <real>] [-multi <int>] [-replex <int>] [-nex <int>]
                    [-reseed <int>]

DESCRIPTION

       This  version  of  the  program  will  only  run while using the OpenMPI parallel computing library.  See
       mpirun(1).  Use the normal gmx(1) program for conventional single-threaded operations.

       gmx mdrun 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 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 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.

       Finally  some  experimental  algorithms  can  be  tested  when  the  appropriate options have been given.
       Currently under investigation are: polarizability.

       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.

       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.
       This results in an infinite run, terminated only when the time limit set by -maxh is reached  (if  any)or
       upon receiving a signal.

       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 ranks is sufficient, this signal should not be sent to  mpirun  or
       the mdrun process that is the parent of the others.

       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.

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

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

       -tabletf [<.xvg>] (tabletf.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 [<dir> [...]] (rundir) (Optional)
              Run directory

       -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

       -devout [<.xvg>] (deviatie.xvg) (Optional)
              xvgr/xmgr file

       -runav [<.xvg>] (runaver.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

       -dn [<.ndx>] (dipole.ndx) (Optional)
              Index file

       -if [<.xvg>] (imdforces.xvg) (Optional)
              xvgr/xmgr file

       -swap [<.xvg>] (swapions.xvg) (Optional)
              xvgr/xmgr file

       Other options:

       -deffnm <string>
              Set the default filename for all file options

       -xvg <enum>
              xvg plot formatting: xmgrace, xmgr, none

       -dd <vector> (0 0 0)
              Domain decomposition grid, 0 is optimize

       -ddorder <enum> (interleave)
              DD rank order: interleave, pp_pme, cartesian

       -npme <int> (-1)
              Number of separate ranks to be used for PME, -1 is guess

       -nt <int> (0)
              Total number of threads to start (0 is guess)

       -ntmpi <int> (0)
              Number of thread-MPI threads to start (0 is guess)

       -ntomp <int> (0)
              Number of OpenMP threads per MPI rank to start (0 is guess)

       -ntomp_pme <int> (0)
              Number of OpenMP threads per MPI rank to start (0 is -ntomp)

       -pin <enum> (auto)
              Whether mdrun should try to set thread affinities: auto, on, off

       -pinoffset <int> (0)
              The lowest logical core number to which mdrun should pin the first thread

       -pinstride <int> (0)
              Pinning  distance  in  logical  cores  for  threads,  use  0 to minimize the number of threads per
              physical core

       -gpu_id <string>
              List of GPU device id-s to use, specifies the per-node PP rank to GPU mapping

       -[no]ddcheck (yes)
              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, yes

       -dds <real> (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.

       -gcom <int> (-1)
              Global communication frequency

       -nb <enum> (auto)
              Calculate non-bonded interactions on: auto, cpu, gpu, gpu_cpu

       -nstlist <int> (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

       -[no]v (no)
              Be loud and noisy

       -[no]compact (yes)
              Write a compact log file

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

       -[no]reprod (no)
              Try to avoid optimizations that affect binary reproducibility

       -cpt <real> (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 <int> (-2)
              Run this number of steps, overrides .mdp file option (-1 means infinite, -2 means use mdp  option,
              smaller is invalid)

       -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 periodically with this period (steps)

       -nex <int> (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 <int> (-1)
              Seed for replica exchange, -1 is generate a seed

SEE ALSO

       gmx(1)

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

       2015, GROMACS development team