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gmx-polystat(1)			GROMACS	Manual		       gmx-polystat(1)

NAME
       gmx-polystat - Calculate	static properties of polymers

SYNOPSIS
       gmx polystat [-s	[<.tpr/.tpb/...>]] [-f [<.xtc/.trr/...>]]
		    [-n	[<.ndx>]] [-o [<.xvg>]]	[-v [<.xvg>]] [-p [<.xvg>]]
		    [-i	[<.xvg>]] [-nice <int>]	[-b <time>] [-e	<time>]
		    [-dt <time>] [-tu <enum>] [-[no]w] [-xvg <enum>]
		    [-[no]mw] [-[no]pc]

DESCRIPTION
       gmx  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	 aver-
       age  gyration  tensor  are written. With	option -v the eigenvectors 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 interpola-
       tion of log(cos).

OPTIONS
       Options to specify input	and output files:

       -s [_.tpr/.tpb/..._] (topol.tpr)	(Input)
	   Run input file: tpr tpb tpa

       -f [_.xtc/.trr/..._] (traj.xtc) (Input)
	   Trajectory: xtc trr cpt trj gro g96 pdb tng

       -n [_.ndx_] (index.ndx) (Input, Optional)
	   Index file

       -o [_.xvg_] (polystat.xvg) (Output)
	   xvgr/xmgr file

       -v [_.xvg_] (polyvec.xvg) (Output, Optional)
	   xvgr/xmgr file

       -p [_.xvg_] (persist.xvg) (Output, Optional)
	   xvgr/xmgr file

       -i [_.xvg_] (intdist.xvg) (Output, Optional)
	   xvgr/xmgr file

       Other options:

       -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, s

       -[no]w  (no)
	   View	output .xvg, .xpm, .eps	and .pdb files

       -xvg _enum_ (xmgrace)
	   xvg plot formatting:	xmgrace, xmgr, none

       -[no]mw	(yes)
	   Use the mass	weighting for radii of gyration

       -[no]pc	(no)
	   Plot	average	eigenvalues

SEE ALSO
       gromacs(7)

       More  information  about	 GROMACS  is  available	 at   <http://www.gro-
       macs.org/>.

VERSION	5.0.6						       gmx-polystat(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO

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