Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
GMX-EXTRACT-CLUSTER(1)		    GROMACS		GMX-EXTRACT-CLUSTER(1)

NAME
       gmx-extract-cluster  -  Allows extracting frames	corresponding to clus-
       ters from trajectory

SYNOPSIS
	  gmx extract-cluster [-f [_.xtc/.trr/..._]] [-s [_.tpr/.gro/..._]]
		       [-n [_.ndx_]] [-clusters	[_.ndx_]]
		       [-o [_.xtc/.trr/..._]] [-b _time_] [-e _time_]
		       [-dt _time_] [-tu _enum_] [-fgroup _selection_]
		       [-xvg _enum_] [-[no]rmpbc] [-[no]pbc] [-sf _file_]
		       [-selrpos _enum_] [-select _selection_] [-vel _enum_]
		       [-force _enum_] [-atoms _enum_] [-precision _int_]
		       [-starttime _time_] [-timestep _time_] [-box _vector_]

DESCRIPTION
       gmx extract-cluster can be used to extract trajectory frames that  cor-
       respond	to  clusters obtained from running gmx cluster with the	-clndx
       option.	The module supports writing all	GROMACS	 supported  trajectory
       file formats.

       Included	 is  also a selection of possible options to change additional
       information.

       It is possible to write only a selection	of atoms to the	output trajec-
       tory files for each cluster.

OPTIONS
       Options to specify input	files:

       -f [<.xtc/.trr/^a|>] (traj.xtc) (Optional)
	      Input  trajectory	 or  single configuration: xtc trr cpt gro g96
	      pdb tng

       -s [<.tpr/.gro/^a|>] (topol.tpr) (Optional)
	      Input structure: tpr gro g96 pdb brk ent

       -n [<.ndx>] (index.ndx) (Optional)
	      Extra index groups

       -clusters [<.ndx>] (cluster.ndx)
	      Name of index file containing frame indices  for	each  cluster,
	      obtained from gmx	cluster	-clndx.

       Options to specify output files:

       -o [<.xtc/.trr/^a|>] (trajout.xtc)
	      Prefix  for  the	name  of  the trajectory file written for each
	      cluster.:	xtc trr	cpt gro	g96 pdb	tng

       Other options:

       -b <time> (0)
	      First frame (ps) to read from trajectory

       -e <time> (0)
	      Last frame (ps) to read from trajectory

       -dt <time> (0)
	      Only use frame if	t MOD dt == first time (ps)

       -tu <enum> (ps)
	      Unit for time values: fs,	ps, ns,	us, ms,	s

       -fgroup <selection>
	      Atoms stored in the trajectory file (if not set, assume first  N
	      atoms)

       -xvg <enum> (xmgrace)
	      Plot formatting: none, xmgrace, xmgr

       -[no]rmpbc (yes)
	      Make molecules whole for each frame

       -[no]pbc	(yes)
	      Use periodic boundary conditions for distance calculation

       -sf <file>
	      Provide selections from files

       -selrpos	<enum> (atom)
	      Selection	 reference positions: atom, res_com, res_cog, mol_com,
	      mol_cog,	  whole_res_com,     whole_res_cog,	whole_mol_com,
	      whole_mol_cog,	part_res_com,	 part_res_cog,	 part_mol_com,
	      part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog

       -select <selection>
	      Selection	of atoms to write to the file

       -vel <enum> (preserved-if-present)
	      Save velocities from frame  if  possible:	 preserved-if-present,
	      always, never

       -force <enum> (preserved-if-present)
	      Save  forces  from  frame	if possible: preserved-if-present, al-
	      ways, never

       -atoms <enum> (preserved-if-present)
	      Decide on	providing new atom information from topology or	 using
	      current	frame	atom  information:  preserved-if-present,  al-
	      ways-from-structure, never, always

       -precision <int>	(3)
	      Set output precision to custom value

       -starttime <time> (0)
	      Change start time	for first frame

       -timestep <time>	(0)
	      Change time between different frames

       -box <vector>
	      New diagonal box vector for output frame

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-EXTRACT-CLUSTER(1)

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

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=gmx-extract-cluster&sektion=1&manpath=FreeBSD+13.0-RELEASE+and+Ports>

home | help