NAME

       gmx-freevolume - Calculate free volume

SYNOPSIS

          gmx freevolume [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]]
                       [-n [<.ndx>]] [-o [<.xvg>]] [-b <time>] [-e <time>]
                       [-dt <time>] [-tu <enum>] [-fgroup <selection>]
                       [-xvg <enum>] [-[no]rmpbc] [-sf <file>]
                       [-selrpos <enum>] [-select <selection>] [-radius <real>]
                       [-seed <int>] [-ninsert <int>]

DESCRIPTION

       gmx freevolume calculates the free volume in a box as a function of time. The free volume is plotted as a
       fraction  of  the  total  volume.   The  program  tries  to  insert a probe with a given radius, into the
       simulations box and if the distance between the probe and any atom is less than the sums of the  van  der
       Waals  radii  of  both  atoms, the position is considered to be occupied, i.e. non-free. By using a probe
       radius of 0, the true free volume is  computed.   By  using  a  larger  radius,  e.g.  0.14  nm,  roughly
       corresponding  to  a  water  molecule, the free volume for a hypothetical particle with that size will be
       produced.  Note however, that since atoms are treated as hard-spheres these number are very  approximate,
       and  typically  only  relative  changes  are meaningful, for instance by doing a series of simulations at
       different temperature.

       The group specified by the  selection  is  considered  to  delineate  non-free  volume.   The  number  of
       insertions  per  unit of volume is important to get a converged result. About 1000/nm^3 yields an overall
       standard deviation that is  determined  by  the  fluctuations  in  the  trajectory  rather  than  by  the
       fluctuations due to the random numbers.

       The  results  are  critically dependent on the van der Waals radii; we recommend to use the values due to
       Bondi (1964).

       The Fractional Free Volume (FFV) that some authors like to use is given by 1 - 1.3*(1-Free Volume).  This
       value is printed on the terminal.

OPTIONS

       Options to specify input files:

       -f [<.xtc/.trr/...>] (traj.xtc) (Optional)
              Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng

       -s [<.tpr/.gro/...>] (topol.tpr) (Optional)
              Input structure: tpr gro g96 pdb brk ent

       -n [<.ndx>] (index.ndx) (Optional)
              Extra index groups

       Options to specify output files:

       -o [<.xvg>] (freevolume.xvg) (Optional)
              Computed free volume

       Other options:

       -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 if t MOD dt == first time (ps)

       -tu <enum> (ps)
              Unit for time values: fs, ps, ns, us, ms, s

       -fgroup <selection>
              Atoms stored in the trajectory file (if not set, assume first N atoms)

       -xvg <enum> (xmgrace)
              Plot formatting: none, xmgrace, xmgr

       -[no]rmpbc (yes)
              Make molecules whole for each frame

       -sf <file>
              Provide selections from files

       -selrpos <enum> (atom)
              Selection   reference   positions:   atom,  res_com,  res_cog,  mol_com,  mol_cog,  whole_res_com,
              whole_res_cog,   whole_mol_com,   whole_mol_cog,   part_res_com,    part_res_cog,    part_mol_com,
              part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog

       -select <selection>
              Atoms that are considered as part of the excluded volume

       -radius <real> (0)
              Radius of the probe to be inserted (nm, 0 yields the true free volume)

       -seed <int> (0)
              Seed for random number generator (0 means generate).

       -ninsert <int> (1000)
              Number of probe insertions per cubic nm to try for each frame in the trajectory.

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2020, GROMACS development team

2020.1-Ubuntu-2020.1-1                            Mar 08, 2020                                 GMX-FREEVOLUME(1)