g_polystat(1) [debian man page]
g_polystat(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_polystat(1) NAME
g_polystat - calculates static properties of polymers VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_polystat -s topol.tpr -f traj.xtc -n index.ndx -o polystat.xvg -v polyvec.xvg -p persist.xvg -i intdist.xvg -[no]h -[no]version -nice int -b time -e time -dt time -tu enum -[no]w -xvg enum -[no]mw -[no]pc DESCRIPTION
g_polystat plots static properties of polymers as a function of time and prints the average. By default it determines the average end-to-end distance and radii of gyration of polymers. It asks for an index group and split this into molecules. The end-to-end distance is then determined using the first and the last atom in the index group for each molecules. For the radius of gyration the total and the three principal components for the average gyration tensor are written. With option -v the eigenvec- tors are written. With option -pc also the average eigenvalues of the individual gyration tensors are written. With option -i the mean square internal distances are written. With option -p the persistence length is determined. The chosen index group should consist of atoms that are consecutively bonded in the polymer mainchains. The persistence length is then determined from the cosine of the angles between bonds with an index difference that is even, the odd pairs are not used, because straight polymer backbones are usually all trans and therefore only every second bond aligns. The persistence length is defined as number of bonds where the average cos reaches a value of 1/e. This point is determined by a linear interpolation of log(cos). FILES
-s topol.tpr Input Run input file: tpr tpb tpa -f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -n index.ndx Input, Opt. Index file -o polystat.xvg Output xvgr/xmgr file -v polyvec.xvg Output, Opt. xvgr/xmgr file -p persist.xvg Output, Opt. xvgr/xmgr file -i intdist.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) -tu enum ps Time unit: fs, ps, ns, us, ms or s -[no]wno View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]mwyes Use the mass weighting for radii of gyration -[no]pcno Plot average eigenvalues SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_polystat(1)
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g_traj(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_traj(1) NAME
g_traj - plots x, v and f of selected atoms/groups (and more) from a trajectory VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_traj -f traj.xtc -s topol.tpr -n index.ndx -ox coord.xvg -oxt coord.xtc -ov veloc.xvg -of force.xvg -ob box.xvg -ot temp.xvg -ekt ektrans.xvg -ekr ekrot.xvg -vd veldist.xvg -cv veloc.pdb -cf force.pdb -av all_veloc.xvg -af all_force.xvg -[no]h -[no]version -nice int -b time -e time -dt time -tu enum -[no]w -xvg enum -[no]com -[no]pbc -[no]mol -[no]nojump -[no]x -[no]y -[no]z -ng int -[no]len -[no]fp -bin real -ctime real -scale real DESCRIPTION
g_traj plots coordinates, velocities, forces and/or the box. With -com the coordinates, velocities and forces are calculated for the center of mass of each group. When -mol is set, the numbers in the index file are interpreted as molecule numbers and the same procedure as with -com is used for each molecule. Option -ot plots the temperature of each group, provided velocities are present in the trajectory file. No corrections are made for con- strained degrees of freedom! This implies -com. Options -ekt and -ekr plot the translational and rotational kinetic energy of each group, provided velocities are present in the trajec- tory file. This implies -com. Options -cv and -cf write the average velocities and average forces as temperature factors to a .pdb file with the average coordinates or the coordinates at -ctime. The temperature factors are scaled such that the maximum is 10. The scaling can be changed with the option -scale. To get the velocities or forces of one frame set both -b and -e to the time of desired frame. When averaging over frames you might need to use the -nojump option to obtain the correct average coordinates. If you select either of these option the average force and velocity for each atom are written to an .xvg file as well (specified with -av or -af). Option -vd computes a velocity distribution, i.e. the norm of the vector is plotted. In addition in the same graph the kinetic energy dis- tribution is given. 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 -ox coord.xvg Output, Opt. xvgr/xmgr file -oxt coord.xtc Output, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -ov veloc.xvg Output, Opt. xvgr/xmgr file -of force.xvg Output, Opt. xvgr/xmgr file -ob box.xvg Output, Opt. xvgr/xmgr file -ot temp.xvg Output, Opt. xvgr/xmgr file -ekt ektrans.xvg Output, Opt. xvgr/xmgr file -ekr ekrot.xvg Output, Opt. xvgr/xmgr file -vd veldist.xvg Output, Opt. xvgr/xmgr file -cv veloc.pdb Output, Opt. Protein data bank file -cf force.pdb Output, Opt. Protein data bank file -av all_veloc.xvg Output, Opt. xvgr/xmgr file -af all_force.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) -tu enum ps Time unit: fs, ps, ns, us, ms or s -[no]wno View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]comno Plot data for the com of each group -[no]pbcyes Make molecules whole for COM -[no]molno Index contains molecule numbers iso atom numbers -[no]nojumpno Remove jumps of atoms across the box -[no]xyes Plot X-component -[no]yyes Plot Y-component -[no]zyes Plot Z-component -ng int 1 Number of groups to consider -[no]lenno Plot vector length -[no]fpno Full precision output -bin real 1 Binwidth for velocity histogram (nm/ps) -ctime real -1 Use frame at this time for x in -cv and -cf instead of the average x -scale real 0 Scale factor for .pdb output, 0 is autoscale SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_traj(1)