Provided by: gromacs-data_2019.3-2_all bug

NAME

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

SYNOPSIS

          gmx mdrun [-s [<.tpr>]] [-cpi [<.cpt>]] [-table [<.xvg>]]
                    [-tablep [<.xvg>]] [-tableb [<.xvg> [...]]]
                    [-rerun [<.xtc/.trr/...>]] [-ei [<.edi>]]
                    [-multidir [<dir> [...]]] [-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>]] [-devout [<.xvg>]]
                    [-runav [<.xvg>]] [-px [<.xvg>]] [-pf [<.xvg>]]
                    [-ro [<.xvg>]] [-ra [<.log>]] [-rs [<.log>]] [-rt [<.log>]]
                    [-mtx [<.mtx>]] [-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>]
                    [-gputasks <string>] [-[no]ddcheck] [-rdd <real>]
                    [-rcon <real>] [-dlb <enum>] [-dds <real>] [-gcom <int>]
                    [-nb <enum>] [-nstlist <int>] [-[no]tunepme] [-pme <enum>]
                    [-pmefft <enum>] [-bonded <enum>] [-[no]v] [-pforce <real>]
                    [-[no]reprod] [-cpt <real>] [-[no]cpnum] [-[no]append]
                    [-nsteps <int>] [-maxh <real>] [-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 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.

       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. 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.

       When  mdrun  receives  a TERM or INT signal (e.g. when ctrl+C is pressed), it will stop at
       the next neighbor search step or  at  the  second  global  communication  step,  whichever
       happens later.  When mdrun receives a second TERM or INT signal and reproducibility is not
       requested, it will stop at the first global communication step.  In  both  cases  all  the
       usual  output  will  be written to file and a checkpoint file is written at the last step.
       When mdrun receives an ABRT signal or the third TERM or INT signal, it will abort directly
       without  writing  a  new  checkpoint  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

       -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

       -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

       -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

       -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> (xmgrace)
              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 ranks 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 unique GPU device IDs available to use

       -gputasks <string>
              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 <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

       -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 (only  with  the  Verlet  cut-off
              scheme)

       -pme <enum> (auto)
              Perform PME calculations on: auto, cpu, gpu

       -pmefft <enum> (auto)
              Perform PME FFT calculations on: auto, cpu, gpu

       -bonded <enum> (auto)
              Perform bonded calculations on: auto, cpu, gpu

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

       -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 (-1 means infinite, -2 means use mdp  option,  smaller  is
              invalid)

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

       -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/>.

COPYRIGHT

       2019, GROMACS development team