1GMX-FREEVOLUME(1)                   GROMACS                  GMX-FREEVOLUME(1)
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NAME

6       gmx-freevolume - Calculate free volume
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SYNOPSIS

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

17       gmx  freevolume  calculates  the  free volume in a box as a function of
18       time. The free volume is plotted as a fraction  of  the  total  volume.
19       The program tries to insert a probe with a given radius, into the simu‐
20       lations box and if the distance between the probe and any atom is  less
21       than the sums of the van der Waals radii of both atoms, the position is
22       considered to be occupied, i.e. non-free. By using a probe radius of 0,
23       the  true free volume is computed.  By using a larger radius, e.g. 0.14
24       nm, roughly corresponding to a water molecule, the free  volume  for  a
25       hypothetical  particle  with that size will be produced.  Note however,
26       that since atoms are treated as  hard-spheres  these  number  are  very
27       approximate,  and  typically  only relative changes are meaningful, for
28       instance by doing a series of simulations at different temperature.
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30       The group  specified  by  the  selection  is  considered  to  delineate
31       non-free volume.  The number of insertions per unit of volume is impor‐
32       tant to get a converged result. About 1000/nm^3 yields an overall stan‐
33       dard deviation that is determined by the fluctuations in the trajectory
34       rather than by the fluctuations due to the random numbers.
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36       The results are critically dependent on the van  der  Waals  radii;  we
37       recommend to use the values due to Bondi (1964).
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39       The Fractional Free Volume (FFV) that some authors like to use is given
40       by 1 - 1.3*(1-Free Volume). This value is printed on the terminal.
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OPTIONS

43       Options to specify input files:
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45       -f [<.xtc/.trr/…>] (traj.xtc) (Optional)
46              Input trajectory or single configuration: xtc trr  cpt  gro  g96
47              pdb tng
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49       -s [<.tpr/.gro/…>] (topol.tpr) (Optional)
50              Input structure: tpr gro g96 pdb brk ent
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52       -n [<.ndx>] (index.ndx) (Optional)
53              Extra index groups
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55       Options to specify output files:
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57       -o [<.xvg>] (freevolume.xvg) (Optional)
58              Computed free volume
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60       Other options:
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62       -b <time> (0)
63              First frame (ps) to read from trajectory
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65       -e <time> (0)
66              Last frame (ps) to read from trajectory
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68       -dt <time> (0)
69              Only use frame if t MOD dt == first time (ps)
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71       -tu <enum> (ps)
72              Unit for time values: fs, ps, ns, us, ms, s
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74       -fgroup <selection>
75              Atoms  stored in the trajectory file (if not set, assume first N
76              atoms)
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78       -xvg <enum> (xmgrace)
79              Plot formatting: none, xmgrace, xmgr
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81       -[no]rmpbc (yes)
82              Make molecules whole for each frame
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84       -sf <file>
85              Provide selections from files
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87       -selrpos <enum> (atom)
88              Selection reference positions: atom, res_com, res_cog,  mol_com,
89              mol_cog,     whole_res_com,     whole_res_cog,    whole_mol_com,
90              whole_mol_cog,   part_res_com,    part_res_cog,    part_mol_com,
91              part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
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93       -select <selection>
94              Atoms that are considered as part of the excluded volume
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96       -radius <real> (0)
97              Radius  of  the probe to be inserted (nm, 0 yields the true free
98              volume)
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100       -seed <int> (0)
101              Seed for random number generator (0 means generate).
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103       -ninsert <int> (1000)
104              Number of probe insertions per cubic nm to try for each frame in
105              the trajectory.
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SEE ALSO

108       gmx(1)
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110       More     information    about    GROMACS    is    available    at    <‐
111       http://www.gromacs.org/>.
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114       2019, GROMACS development team
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1192019.2                           Apr 16, 2019                GMX-FREEVOLUME(1)
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