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

NAME
g_nmens - generates an ensemble of structures from the normal modes VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_nmens -v eigenvec.trr -e eigenval.xvg -s topol.tpr -n index.ndx -o ensemble.xtc -[no]h -[no]version -nice int -xvg enum -temp real -seed int -num int -first int -last int DESCRIPTION
g_nmens generates an ensemble around an average structure in a subspace that is defined by a set of normal modes (eigenvectors). The eigenvectors are assumed to be mass-weighted. The position along each eigenvector is randomly taken from a Gaussian distribution with variance kT/eigenvalue. By default the starting eigenvector is set to 7, since the first six normal modes are the translational and rotational degrees of freedom. FILES
-v eigenvec.trr Input Full precision trajectory: trr trj cpt -e eigenval.xvg Input xvgr/xmgr file -s topol.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb -n index.ndx Input, Opt. Index file -o ensemble.xtc Output Trajectory: xtc trr trj gro g96 pdb OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno Print version info and quit -nice int 19 Set the nicelevel -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -temp real 300 Temperature in Kelvin -seed int -1 Random seed, -1 generates a seed from time and pid -num int 100 Number of structures to generate -first int 7 First eigenvector to use (-1 is select) -last int -1 Last eigenvector to use (-1 is till the last) SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_nmens(1)

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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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