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GMX-MDRUN(1)			    GROMACS			  GMX-MDRUN(1)

NAME
       gmx-mdrun  -  Perform a simulation, do a	normal mode analysis or	an en-
       ergy 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_]] [-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_]
		    [-nb _enum_] [-nstlist _int_] [-[no]tunepme] [-pme _enum_]
		    [-pmefft _enum_] [-bonded _enum_] [-update _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	inser-
       tion  or	 (re)calculation of energies.  Normal mode analysis is another
       option. In this case mdrun builds a Hessian matrix from single  confor-
       mation.	 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 co-
       ordinates 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 po-
       tential 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, interac-
       tion 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 se-
       quence before the file extension. That sequence is: an underscore, then
       a aba for bonds,	an aaa for angles or a ada 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	check-
       point  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  append-
       ing  to	the existing output files. The checkpoint file contains	check-
       sums of all output files, such that you will never loose	data when some
       output files are	modified, corrupt or removed.  There are three scenar-
       ios with	-cpi:

       * no files with matching	names are present: new output files are	 writ-
       ten

       *  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 num-
       ber  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  ap-
       pending	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	termi-
       nate  the  simulation  from the molecular viewer	(e.g. VMD). With -imd-
       wait, 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 in-
       dices 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> [^a|]] (table.xvg) (Optional)
	      xvgr/xmgr	file

       -rerun [<.xtc/.trr/^a|>] (rerun.xtc) (Optional)
	      Trajectory: xtc trr cpt gro g96 pdb tng

       -ei [<.edi>] (sam.edi) (Optional)
	      ED sampling input

       -multidir [<dir>	[^a|]] (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/^a|>] (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/^a|>] (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 <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.

       -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

       -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

       -update <enum> (auto)
	      Perform update and constraints 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
       2020, GROMACS development team

2020.4				 Oct 06, 2020			  GMX-MDRUN(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT

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