xenial (1) gmx-mdrun.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

       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