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g_bond(1) [debian man page]

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

NAME

       g_bond - calculates distances between atoms

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_bond  -f  traj.xtc  -n index.ndx -s topol.tpr -o bonds.xvg -l bonds.log -d distance.xvg -[no]h -[no]version -nice int -b time -e time -dt
       time -[no]w -xvg enum -blen real -tol real -[no]aver -[no]averdist

DESCRIPTION

	g_bond makes a distribution of bond lengths. If all is well a Gaussian distribution should be made when using a harmonic potential.  Bonds
       are read from a single group in the index file in order i1-j1 i2-j2 through in-jn.

	-tol gives the half-width of the distribution as a fraction of the bondlength ( -blen). That means, for a bond of 0.2 a tol of 0.1 gives a
       distribution from 0.18 to 0.22.

       Option  -d plots all the distances as a function of time.  This requires a structure file for the atom and residue names in the output.	If
       however the option  -averdist is given (as well or separately) the average bond length is plotted instead.

FILES

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

       -n index.ndx Input
	Index file

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

       -o bonds.xvg Output
	xvgr/xmgr file

       -l bonds.log Output, Opt.
	Log file

       -d distance.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)

       -[no]wno
	View output  .xvg,  .xpm,  .eps and  .pdb files

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

       -blen real -1
	Bond length. By default length of first bond

       -tol real 0.1
	Half width of distribution as fraction of blen

       -[no]averyes
	Average bond length distributions

       -[no]averdistyes
	Average distances (turns on  -d)

KNOWN PROBLEMS

       - It should be possible to get bond information from the topology.

SEE ALSO

       gromacs(7)

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

								  Mon 4 Apr 2011							 g_bond(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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