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


       gmx-insert-molecules - Insert molecules into existing vacancies


          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>]


       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

       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 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,

       -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



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       2018, GROMACS development team