g_mdmat(1) [debian 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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g_vanhove(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_vanhove(1) NAME
g_vanhove - calculates Van Hove displacement functions VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_vanhove -f traj.xtc -s topol.tpr -n index.ndx -om vanhove.xpm -or vanhove_r.xvg -ot vanhove_t.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -sqrt real -fm int -rmax real -rbin real -mmax real -nlevels int -nr int -fr int -rt real -ft int DESCRIPTION
g_vanhove computes the Van Hove correlation function. The Van Hove G(r,t) is the probability that a particle that is at r0 at time zero can be found at position r0+r at time t. g_vanhove determines G not for a vector r, but for the length of r. Thus it gives the probabil- ity that a particle moves a distance of r in time t. Jumps across the periodic boundaries are removed. Corrections are made for scaling due to isotropic or anisotropic pressure coupling. With option -om the whole matrix can be written as a function of t and r or as a function of sqrt(t) and r (option -sqrt). With option -or the Van Hove function is plotted for one or more values of t. Option -nr sets the number of times, option -fr the number spacing between the times. The binwidth is set with option -rbin. The number of bins is determined automatically. With option -ot the integral up to a certain distance (option -rt) is plotted as a function of time. For all frames that are read the coordinates of the selected particles are stored in memory. Therefore the program may use a lot of memory. For options -om and -ot the program may be slow. This is because the calculation scales as the number of frames times -fm or -ft. Note that with the -dt option the memory usage and calculation time can be reduced. 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 -om vanhove.xpm Output, Opt. X PixMap compatible matrix file -or vanhove_r.xvg Output, Opt. xvgr/xmgr file -ot vanhove_t.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 -sqrt real 0 Use sqrt(t) on the matrix axis which binspacing in sqrt(ps) -fm int 0 Number of frames in the matrix, 0 is plot all -rmax real 2 Maximum r in the matrix (nm) -rbin real 0.01 Binwidth in the matrix and for -or (nm) -mmax real 0 Maximum density in the matrix, 0 is calculate (1/nm) -nlevels int 81 Number of levels in the matrix -nr int 1 Number of curves for the -or output -fr int 0 Frame spacing for the -or output -rt real 0 Integration limit for the -ot output (nm) -ft int 0 Number of frames in the -ot output, 0 is plot all SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_vanhove(1)