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