xenial (1) gmx-insert-molecules.1.gz

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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/>.


       2015, GROMACS development team