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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>] [-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 inser- tions. 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 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/...>] (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 2025.0 Feb 10, 2025 GMX-INSERT-MOLECULES(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT
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