Provided by: gromacs-data_2019.3-2_all bug


       gmx-freevolume - Calculate free volume


          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>]


       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 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,

       -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.



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       2019, GROMACS development team