gmx-freevolume(1) GROMACS Manual gmx-freevolume(1)NAMEgmx-freevolume - Calculate free volume
SYNOPSIS
gmx freevolume [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]]
[-n [<.ndx>]] [-o [<.xvg>]] [-b <time>] [-e <time>]
[-dt <time>] [-tu <enum>] [-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 simula‐
tions 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 impor‐
tant to get a converged result. About 1000/nm3 yields an overall stan‐
dard 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 and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input, Optional)
Input trajectory or single configuration: xtc trr cpt trj gro g96
pdb tng
-s [<.tpr/.tpb/...>] (topol.tpr) (Input, Optional)
Input structure: tpr tpb tpa gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Input, Optional)
Extra index groups
-o [<.xvg>] (freevolume.xvg) (Output, 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
-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>
-radius <real> (0)
Radius of the probe to be inserted (nm, 0 yields the true free vol‐
ume)
-seed <int> (-1)
Seed for random number generator.
-ninsert <int> (1000)
Number of probe insertions per cubic nm to try for each frame in
the trajectory.
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-freevolume(1)
