g_rmsdist(1) [debian man page]
g_rmsdist(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_rmsdist(1) NAME
g_rmsdist - calculates atom pair distances averaged with power -2, -3 or -6 VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_rmsdist -f traj.xtc -s topol.tpr -n index.ndx -equiv equiv.dat -o distrmsd.xvg -rms rmsdist.xpm -scl rmsscale.xpm -mean rmsmean.xpm -nmr3 nmr3.xpm -nmr6 nmr6.xpm -noe noe.dat -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -nlevels int -max real -[no]sumh -[no]pbc DESCRIPTION
g_rmsdist computes the root mean square deviation of atom distances, which has the advantage that no fit is needed like in standard RMS deviation as computed by g_rms. The reference structure is taken from the structure file. The RMSD at time t is calculated as the RMS of the differences in distance between atom-pairs in the reference structure and the structure at time t. g_rmsdist can also produce matrices of the rms distances, rms distances scaled with the mean distance and the mean distances and matrices with NMR averaged distances (1/r3 and 1/r6 averaging). Finally, lists of atom pairs with 1/r3 and 1/r6 averaged distance below the maximum distance ( -max, which will default to 0.6 in this case) can be generated, by default averaging over equivalent hydrogens (all triplets of hydrogens named *[123]). Additionally a list of equivalent atoms can be supplied ( -equiv), each line containing a set of equivalent atoms specified as residue number and name and atom name; e.g.: 3 SER HB1 3 SER HB2 Residue and atom names must exactly match those in the structure file, including case. Specifying non-sequential atoms is undefined. 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 -equiv equiv.dat Input, Opt. Generic data file -o distrmsd.xvg Output xvgr/xmgr file -rms rmsdist.xpm Output, Opt. X PixMap compatible matrix file -scl rmsscale.xpm Output, Opt. X PixMap compatible matrix file -mean rmsmean.xpm Output, Opt. X PixMap compatible matrix file -nmr3 nmr3.xpm Output, Opt. X PixMap compatible matrix file -nmr6 nmr6.xpm Output, Opt. X PixMap compatible matrix file -noe noe.dat Output, Opt. Generic data 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 -nlevels int 40 Discretize rms in levels -max real -1 Maximum level in matrices -[no]sumhyes average distance over equivalent hydrogens -[no]pbcyes Use periodic boundary conditions when computing distances SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_rmsdist(1)
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g_covar(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_covar(1) NAME
g_covar - calculates and diagonalizes the covariance matrix VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_covar -f traj.xtc -s topol.tpr -n index.ndx -o eigenval.xvg -v eigenvec.trr -av average.pdb -l covar.log -ascii covar.dat -xpm covar.xpm -xpma covara.xpm -[no]h -[no]version -nice int -b time -e time -dt time -tu enum -xvg enum -[no]fit -[no]ref -[no]mwa -last int -[no]pbc DESCRIPTION
g_covar calculates and diagonalizes the (mass-weighted) covariance matrix. All structures are fitted to the structure in the structure file. When this is not a run input file periodicity will not be taken into account. When the fit and analysis groups are identical and the analysis is non mass-weighted, the fit will also be non mass-weighted. The eigenvectors are written to a trajectory file ( -v). When the same atoms are used for the fit and the covariance analysis, the refer- ence structure for the fit is written first with t=-1. The average (or reference when -ref is used) structure is written with t=0, the eigenvectors are written as frames with the eigenvector number as timestamp. The eigenvectors can be analyzed with g_anaeig. Option -ascii writes the whole covariance matrix to an ASCII file. The order of the elements is: x1x1, x1y1, x1z1, x1x2, ... Option -xpm writes the whole covariance matrix to an .xpm file. Option -xpma writes the atomic covariance matrix to an .xpm file, i.e. for each atom pair the sum of the xx, yy and zz covariances is written. Note that the diagonalization of a matrix requires memory and time that will increase at least as fast as than the square of the number of atoms involved. It is easy to run out of memory, in which case this tool will probably exit with a 'Segmentation fault'. You should con- sider carefully whether a reduced set of atoms will meet your needs for lower costs. 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 -o eigenval.xvg Output xvgr/xmgr file -v eigenvec.trr Output Full precision trajectory: trr trj cpt -av average.pdb Output Structure file: gro g96 pdb etc. -l covar.log Output Log file -ascii covar.dat Output, Opt. Generic data file -xpm covar.xpm Output, Opt. X PixMap compatible matrix file -xpma covara.xpm Output, Opt. X PixMap compatible matrix 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) -tu enum ps Time unit: fs, ps, ns, us, ms or s -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]fityes Fit to a reference structure -[no]refno Use the deviation from the conformation in the structure file instead of from the average -[no]mwano Mass-weighted covariance analysis -last int -1 Last eigenvector to write away (-1 is till the last) -[no]pbcyes Apply corrections for periodic boundary conditions SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_covar(1)