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g_options(1) [debian man page]

g_options(1)						   GROMACS suite, VERSION 4.5.4 					      g_options(1)

NAME

       g_options - Utility program for generating GROMACS documentation VERSION 4.5.4

SYNOPSIS

       g_options -[no]h -[no]version -nice int

DESCRIPTION

       GROMACS programs have some standard options, of which some are hidden by default:

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 0
	Set the nicelevel

KNOWN PROBLEMS

       - If the configuration script found Motif or Lesstif on your system, you can use the graphical interface (if not, you will get an error):
	-X gmx_bool  no Use dialog box GUI to edit command line options

       - When compiled on an SGI-IRIX system, all GROMACS programs have an additional option:
	-npri int  0 Set non blocking priority (try 128)

       -  Optional  files  are	not used unless the option is set, in contrast to non-optional files, where the default file name is used when the
       option is not set.

       - All GROMACS programs will accept file options without a file extension or filename being specified. In such cases the	default  filenames
       will  be used. With multiple input file types, such as generic structure format, the directory will be searched for files of each type with
       the supplied or default name. When no such file is found, or with output files the first file type will be used.

       - All GROMACS programs with the exception of  mdrun and	eneconv check if the command line options are valid.  If this is not the case, the
       program will be halted.

       - Enumerated options (enum) should be used with one of the arguments listed in the option description, the argument may be abbreviated. The
       first match to the shortest argument in the list will be selected.

       - Vector options can be used with 1 or 3 parameters. When only one parameter is supplied the two others are also set to this value.

       - All GROMACS programs can read compressed or g-zipped files. There might be a problem with  reading  compressed   .xtc,   .trr	and   .trj
       files, but these will not compress very well anyway.

       - Most GROMACS programs can process a trajectory with fewer atoms than the run input or structure file, but only if the trajectory consists
       of the first n atoms of the run input or structure file.

       - Many GROMACS programs will accept the	-tu option to set the time units to use in output files (e.g. for  xmgr graphs or   xpm  matrices)
       and in all time options.

SEE ALSO

       gromacs(7)

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

								  Mon 21 Mar 2011						      g_options(1)

Check Out this Related Man Page

g_mdmat(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					g_mdmat(1)

NAME

       g_mdmat - calculates residue contact maps

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_mdmat	-f  traj.xtc  -s topol.tpr -n index.ndx -mean dm.xpm -frames dmf.xpm -no num.xvg -[no]h -[no]version -nice int -b time -e time -dt
       time -xvg enum -t real -nlevels int

DESCRIPTION

	g_mdmat makes distance matrices consisting of the smallest distance between residue pairs. With  -frames, these distance matrices  can	be
       stored  in  order  to see differences in tertiary structure as a function of time. If you choose your options unwisely, this may generate a
       large output file. By default, only an averaged matrix over the whole trajectory is output.  Also a count of the number of different atomic
       contacts between residues over the whole trajectory can be made.  The output can be processed with  xpm2ps to make a PostScript (tm) plot.

FILES

       -f traj.xtc Input
	Trajectory: xtc trr trj gro g96 pdb cpt

       -s topol.tpr Input
	Structure+mass(db): tpr tpb tpa gro g96 pdb

       -n index.ndx Input, Opt.
	Index file

       -mean dm.xpm Output
	X PixMap compatible matrix file

       -frames dmf.xpm Output, Opt.
	X PixMap compatible matrix file

       -no num.xvg Output, Opt.
	xvgr/xmgr file

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 19
	Set the nicelevel

       -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 when t MOD dt = first time (ps)

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -t real 1.5
	trunc distance

       -nlevels int 40
	Discretize distance in	levels

SEE ALSO

       gromacs(7)

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

								  Mon 4 Apr 2011							g_mdmat(1)
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