gmx-polystat - Calculate static properties of polymers

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                   GMX-POLYSTAT(1)

gmxpolystat 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  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 interpolation of log(<cos>).

       gmx-polystat - Calculate static properties of polymers

       Options to specify input files:

       -s[<.tpr>](topol.tpr)
              Portable xdr run input file

       -f[<.xtc/.trr/...>](traj.xtc)
              Trajectory: xtctrrcptgrog96pdbtng-n[<.ndx>](index.ndx)(Optional)
              Index file

       Options to specify output files:

       -o[<.xvg>](polystat.xvg)
              xvgr/xmgr file

       -v[<.xvg>](polyvec.xvg)(Optional)
              xvgr/xmgr file

       -p[<.xvg>](persist.xvg)(Optional)
              xvgr/xmgr file

       -i[<.xvg>](intdist.xvg)(Optional)
              xvgr/xmgr file

       Other options:

       -b<time>(0)
              Time of first frame to read from trajectory (default unit ps)

       -e<time>(0)
              Time of last frame to read from trajectory (default unit ps)

       -dt<time>(0)
              Only use frame when t MOD dt = first time (default unit ps)

       -tu<enum>(ps)
              Unit for time values: 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

gmx(1)

       More information about GROMACS is available at <http://www.gromacs.org/>.

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