debian man page for g_polystat

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)