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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)

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

NAME
g_rmsf - calculates atomic fluctuations VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_rmsf -f traj.xtc -s topol.tpr -n index.ndx -q eiwit.pdb -oq bfac.pdb -ox xaver.pdb -o rmsf.xvg -od rmsdev.xvg -oc correl.xvg -dir rmsf.log -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[no]res -[no]aniso -[no]fit DESCRIPTION
g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions in the trajectory (supplied with -f) after (optionally) fitting to a reference frame (supplied with -s). With option -oq the RMSF values are converted to B-factor values, which are written to a .pdb file with the coordinates, of the structure file, or of a .pdb file when -q is specified. Option -ox writes the B-factors to a file with the average coordinates. With the option -od the root mean square deviation with respect to the reference structure is calculated. With the option -aniso, g_rmsf will compute anisotropic temperature factors and then it will also output average coordinates and a .pdb file with ANISOU records (corresonding to the -oq or -ox option). Please note that the U values are orientation-dependent, so before com- parison with experimental data you should verify that you fit to the experimental coordinates. When a .pdb input file is passed to the program and the -aniso flag is set a correlation plot of the Uij will be created, if any aniso- tropic temperature factors are present in the .pdb file. With option -dir the average MSF (3x3) matrix is diagonalized. This shows the directions in which the atoms fluctuate the most and the least. 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 -q eiwit.pdb Input, Opt. Protein data bank file -oq bfac.pdb Output, Opt. Protein data bank file -ox xaver.pdb Output, Opt. Protein data bank file -o rmsf.xvg Output xvgr/xmgr file -od rmsdev.xvg Output, Opt. xvgr/xmgr file -oc correl.xvg Output, Opt. xvgr/xmgr file -dir rmsf.log Output, Opt. Log 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 -[no]resno Calculate averages for each residue -[no]anisono Compute anisotropic termperature factors -[no]fityes Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure and the trajectory match. SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_rmsf(1)
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