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

Provided by: gromacs-data_2018.1-1_all bug

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>] [-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.

       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

       -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/>.


       2018, GROMACS development team