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

NAME
g_gyrate - calculates the radius of gyration VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_gyrate -f traj.xtc -s topol.tpr -n index.ndx -o gyrate.xvg -acf moi-acf.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -nmol int -[no]q -[no]p -[no]moi -nz int -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real DESCRIPTION
g_gyrate computes the radius of gyration of a group of atoms and the radii of gyration about the x-, y- and z-axes, as a function of time. The atoms are explicitly mass weighted. With the -nmol option the radius of gyration will be calculated for multiple molecules by splitting the analysis group in equally sized parts. With the option -nz 2D radii of gyration in the x-y plane of slices along the z-axis are calculated. 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 gyrate.xvg Output xvgr/xmgr file -acf moi-acf.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) -[no]wno View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -nmol int 1 The number of molecules to analyze -[no]qno Use absolute value of the charge of an atom as weighting factor instead of mass -[no]pno Calculate the radii of gyration about the principal axes. -[no]moino Calculate the moments of inertia (defined by the principal axes). -nz int 0 Calculate the 2D radii of gyration of slices along the z-axis -acflen int -1 Length of the ACF, default is half the number of frames -[no]normalizeyes Normalize ACF -P enum 0 Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3 -fitfn enum none Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7, exp9 or erffit -ncskip int 0 Skip N points in the output file of correlation functions -beginfit real 0 Time where to begin the exponential fit of the correlation function -endfit real -1 Time where to end the exponential fit of the correlation function, -1 is until the end SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_gyrate(1)
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