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GMX-INSERT-MOLECULES(1)		    GROMACS	       GMX-INSERT-MOLECULES(1)

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 dis-
       carded.

       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  in-
       serted molecules	will be	removed	instead	of preventing insertion.

       By default, the insertion positions are random (with initial seed spec-
       ified by	-seed).	The program iterates until -nmol molecules  have  been
       inserted	 in the	box. Molecules are not inserted	where the distance be-
       tween 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 data-
       base, 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/^a|>] (protein.gro) (Optional)
	      Existing	configuration  to insert into: gro g96 pdb brk ent esp
	      tpr

       -ci [<.gro/.g96/^a|>] (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/^a|>] (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/>.

COPYRIGHT
       2020, GROMACS development team

2020.4				 Oct 06, 2020	       GMX-INSERT-MOLECULES(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT

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