1GMX-INSERT-MOLECULES(1) GROMACS GMX-INSERT-MOLECULES(1)
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6 gmx-insert-molecules - Insert molecules into existing vacancies
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9 gmx insert-molecules [-f [<.gro/.g96/...>]] [-ci [<.gro/.g96/...>]]
10 [-ip [<.dat>]] [-n [<.ndx>]] [-o [<.gro/.g96/...>]]
11 [-replace <selection>] [-sf <file>] [-selrpos <enum>]
12 [-box <vector>] [-nmol <int>] [-try <int>] [-seed <int>]
13 [-radius <real>] [-scale <real>] [-dr <vector>]
14 [-rot <enum>]
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17 gmx insert-molecules inserts -nmol copies of the system specified in
18 the -ci input file. The insertions take place either into vacant space
19 in the solute conformation given with -f, or into an empty box given by
20 -box. Specifying both -f and -box behaves like -f, but places a new box
21 around the solute before insertions. Any velocities present are dis‐
22 carded.
23 It is possible to also insert into a solvated configuration and replace
25 solvent atoms with the inserted atoms. To do this, use -replace to
26 specify a selection that identifies the atoms that can be replaced. The
27 tool assumes that all molecules in this selection consist of single
28 residues: each residue from this selection that overlaps with the in‐
29 serted molecules will be removed instead of preventing insertion.
30 By default, the insertion positions are random (with initial seed spec‐
32 ified by -seed). The program iterates until -nmol molecules have been
33 inserted in the box. Molecules are not inserted where the distance be‐
34 tween any existing atom and any atom of the inserted molecule is less
35 than the sum based on the van der Waals radii of both atoms. A database
36 (vdwradii.dat) of van der Waals radii is read by the program, and the
37 resulting radii scaled by -scale. If radii are not found in the data‐
38 base, those atoms are assigned the (pre-scaled) distance -radius. Note
39 that the usefulness of those radii depends on the atom names, and thus
40 varies widely with force field.
41 A total of -nmol * -try insertion attempts are made before giving up.
43 Increase -try if you have several small holes to fill. Option -rot
44 specifies whether the insertion molecules are randomly oriented before
45 insertion attempts.
46 Alternatively, the molecules can be inserted only at positions defined
48 in positions.dat (-ip). That file should have 3 columns (x,y,z), that
49 give the displacements compared to the input molecule position (-ci).
50 Hence, if that file should contain the absolute positions, the molecule
51 must be centered on (0,0,0) before using gmx insert-molecules (e.g.
52 from gmx editconf -center). Comments in that file starting with # are
53 ignored. Option -dr defines the maximally allowed displacements during
54 insertial trials. -try and -rot work as in the default mode (see
55 above).
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58 Options to specify input files:
59 -f [<.gro/.g96/...>] (protein.gro) (Optional)
61 Existing configuration to insert into: gro g96 pdb brk ent esp
62 tpr
63 -ci [<.gro/.g96/...>] (insert.gro)
65 Configuration to insert: gro g96 pdb brk ent esp tpr
66 -ip [<.dat>] (positions.dat) (Optional)
68 Predefined insertion trial positions
69 -n [<.ndx>] (index.ndx) (Optional)
71 Extra index groups
72 Options to specify output files:
74 -o [<.gro/.g96/...>] (out.gro)
76 Output configuration after insertion: gro g96 pdb brk ent esp
77 Other options:
79 -replace <selection>
81 Atoms that can be removed if overlapping
82 -sf <file>
84 Provide selections from files
85 -selrpos <enum> (atom)
87 Selection reference positions: atom, res_com, res_cog, mol_com,
88 mol_cog, whole_res_com, whole_res_cog, whole_mol_com,
89 whole_mol_cog, part_res_com, part_res_cog, part_mol_com,
90 part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
91 -box <vector> (0 0 0)
93 Box size (in nm)
94 -nmol <int> (0)
96 Number of extra molecules to insert
97 -try <int> (10)
99 Try inserting -nmol times -try times
100 -seed <int> (0)
102 Random generator seed (0 means generate)
103 -radius <real> (0.105)
105 Default van der Waals distance
106 -scale <real> (0.57)
108 Scale factor to multiply Van der Waals radii from the database
109 in share/gromacs/top/vdwradii.dat. The default value of 0.57
110 yields density close to 1000 g/l for proteins in water.
111 -dr <vector> (0 0 0)
113 Allowed displacement in x/y/z from positions in -ip file
114 -rot <enum> (xyz)
116 Rotate inserted molecules randomly: xyz, z, none
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119 gmx(1)
120 More information about GROMACS is available at <‐
122 http://www.gromacs.org/>.
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125 2022, GROMACS development team
1262022.3 Sep 02, 2022 GMX-INSERT-MOLECULES(1)