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g_morph(1) [debian man page]

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

NAME

       g_morph - linear interpolation of conformations

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_morph	-f1  conf1.gro -f2 conf2.gro -o interm.xtc -or rms-interm.xvg -n index.ndx -[no]h -[no]version -nice int -[no]w -xvg enum -ninterm
       int -first real -last real -[no]fit

DESCRIPTION

	g_morph does a linear interpolation of conformations in order to create intermediates. Of course these are completely unphysical, but that
       you  may  try  to  justify  yourself. Output is in the form of a generic trajectory. The number of intermediates can be controlled with the
       -ninterm flag. The first and last flag correspond to the way of interpolating: 0 corresponds to input structure 1 while	1  corresponds	to
       input structure 2.  If you specify  -first  0 or  -last	1 extrapolation will be on the path from input structure x1 to x2. In general, the
       coordinates of the intermediate x(i) out of N total intermidates correspond to:

       x(i) = x1 + (first+(i/(N-1))*(last-first))*(x2-x1)

       Finally the RMSD with respect to both input structures can be computed if explicitly selected ( -or option). In that case,  an  index  file
       may be read to select the group from which the RMS is computed.

FILES

       -f1 conf1.gro Input
	Structure file: gro g96 pdb tpr etc.

       -f2 conf2.gro Input
	Structure file: gro g96 pdb tpr etc.

       -o interm.xtc Output
	Trajectory: xtc trr trj gro g96 pdb cpt

       -or rms-interm.xvg Output, Opt.
	xvgr/xmgr file

       -n index.ndx Input, Opt.
	Index file

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 0
	Set the nicelevel

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

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

       -ninterm int 11
	Number of intermediates

       -first real 0
	Corresponds to first generated structure (0 is input x0, see above)

       -last real 1
	Corresponds to last generated structure (1 is input x1, see above)

       -[no]fityes
	Do a least squares fit of the second to the first structure before interpolating

SEE ALSO

       gromacs(7)

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

								  Mon 4 Apr 2011							g_morph(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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