NAME

       gmx-insert-molecules - Insert molecules into existing vacancies

SYNOPSIS

          gmx insert-molecules [-f [<.gro/.g96/...>]] [-ci [<.gro/.g96/...>]]
                       [-ip [<.dat>]] [-n [<.ndx>]] [-o [<.gro/.g96/...>]]
                       [-replace <selection>] [-sf <file>] [-selrpos <enum>]
                       [-box <vector>] [-nmol <int>] [-conc <real>]
                       [-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 number of
       copies can also be determined by the concentration -conc in mol/liter and  box  volume.   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.

       It  is  possible to also insert into a solvated configuration and replace solvent atoms with the inserted
       atoms. To do this, use -replace to specify a selection that identifies the atoms that  can  be  replaced.
       The  tool assumes that all molecules in this selection consist of single residues: each residue from this
       selection that overlaps with the inserted molecules will be removed instead of preventing insertion.

       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,  those  atoms
       are  assigned  the (pre-scaled) distance -radius.  Note that the usefulness of those radii depends on the
       atom names, and thus varies widely with force field.

       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

       -n [<.ndx>] (index.ndx) (Optional)
              Extra index groups

       Options to specify output files:

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

       Other options:

       -replace <selection>
              Atoms that can be removed if overlapping

       -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

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

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

       -conc <real> (0)
              Concentration (in mol/liter) of extra molecules to insert. This overrides -nmol

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

       -seed <int> (0)
              Random generator seed (0 means generate)

       -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> (xyz)
              Rotate inserted molecules randomly: xyz, z, none

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2025, GROMACS development team

2025.2                                            May 12, 2025                           GMX-INSERT-MOLECULES(1)