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

NAME
g_rotmat - plots the rotation matrix for fitting to a reference structure VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_rotmat -f traj.xtc -s topol.tpr -n index.ndx -o rotmat.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -ref enum -skip int -[no]fitxy -[no]mw DESCRIPTION
g_rotmat plots the rotation matrix required for least squares fitting a conformation onto the reference conformation provided with -s. Translation is removed before fitting. The output are the three vectors that give the new directions of the x, y and z directions of the reference conformation, for example: (zx,zy,zz) is the orientation of the reference z-axis in the trajectory frame. This tool is useful for, for instance, determining the orientation of a molecule at an interface, possibly on a trajectory produced with trjconv -fit rotxy+transxy to remove the rotation in the x-y plane. Option -ref determines a reference structure for fitting, instead of using the structure from -s. The structure with the lowest sum of RMSD's to all other structures is used. Since the computational cost of this procedure grows with the square of the number of frames, the -skip option can be useful. A full fit or only a fit in the x-y plane can be performed. Option -fitxy fits in the x-y plane before determining the rotation matrix. 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 rotmat.xvg Output 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 -ref enum none Determine the optimal reference structure: none, xyz or xy -skip int 1 Use every nr-th frame for -ref -[no]fitxyno Fit the x/y rotation before determining the rotation -[no]mwyes Use mass weighted fitting SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_rotmat(1)
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