NAME

       gmx-insert-molecules - Insert molecules into existing vacancies

SYNOPSIS

          gmx insert-molecules [-f [<.gro/.g96/...>]] [-ci [<.gro/.g96/...>]]
                       [-ip [<.dat>]] [-o [<.gro/.g96/...>]] [-box <vector>]
                       [-nmol <int>] [-try <int>] [-seed <int>]
                       [-radius <real>] [-scale <real>] [-dr <vector>]
                       [-rot <enum>]

DESCRIPTION

       gmx  insert-molecules  inserts -nmol copies of the system specified in the -ci input file.
       The insertions take place either into vacant space in the solute conformation  given  with
       -f,  or  into an empty box given by -box. Specifying both -f and -box behaves like -f, but
       places a new  box  around  the  solute  before  insertions.  Any  velocities  present  are
       discarded.

       By default, the insertion positions are random (with initial seed specified by -seed). The
       program iterates until -nmol molecules have been inserted in the box.  Molecules  are  not
       inserted  where  the  distance  between  any  existing  atom  and any atom of the inserted
       molecule is less than the sum based on the van der Waals radii of both atoms.  A  database
       (vdwradii.dat)  of  van  der  Waals  radii is read by the program, and the resulting radii
       scaled by -scale. If radii are not found in the  database,  thoseatoms  are  assigned  the
       (pre-scaled) distance -radius.

       A total of -nmol * -try insertion attempts are made before giving up. Increase -try if you
       have several small holes to fill. Option -rot specifies whether  the  insertion  molecules
       are randomly oriented before insertion attempts.

       Alternatively,  the  molecules  can be inserted only at positions defined in positions.dat
       (-ip). That file should have 3 columns (x,y,z), that give the  displacements  compared  to
       the  input  molecule  position  (-ci).  Hence,  if  that  file should contain the absolute
       positions, the molecule must be centered on  (0,0,0)  before  using  gmx  insert-molecules
       (e.g.  from  gmx  editconf  -center).   Comments in that file starting with # are ignored.
       Option -dr defines the maximally allowed displacements during insertial trials.  -try  and
       -rot work as in the default mode (see above).

OPTIONS

       Options to specify input files:

       -f [<.gro/.g96/...>] (protein.gro) (Optional)
              Existing configuration to insert into: gro g96 pdb brk ent esp tpr

       -ci [<.gro/.g96/...>] (insert.gro)
              Configuration to insert: gro g96 pdb brk ent esp tpr

       -ip [<.dat>] (positions.dat) (Optional)
              Predefined insertion trial positions

       Options to specify output files:

       -o [<.gro/.g96/...>] (out.gro)
              Output configuration after insertion: gro g96 pdb brk ent esp

       Other options:

       -box <vector> (0 0 0)
              Box size (in nm)

       -nmol <int> (0)
              Number of extra molecules to insert

       -try <int> (10)
              Try inserting -nmol times -try times

       -seed <int> (1997)
              Random generator seed

       -radius <real> (0.105)
              Default van der Waals distance

       -scale <real> (0.57)
              Scale   factor   to   multiply   Van   der   Waals   radii  from  the  database  in
              share/gromacs/top/vdwradii.dat. The default value of 0.57 yields density  close  to
              1000 g/l for proteins in water.

       -dr <vector> (0 0 0)
              Allowed displacement in x/y/z from positions in -ip file

       -rot <enum>
              Rotate inserted molecules randomly: xyz, z, none

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2015, GROMACS development team