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

6       gmx-insert-molecules - Insert molecules into existing vacancies
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SYNOPSIS

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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DESCRIPTION

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.
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24       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
29       inserted molecules will be removed instead of preventing insertion.
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31       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
34       between 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.
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42       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.
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47       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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OPTIONS

58       Options to specify input files:
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60       -f [<.gro/.g96/…>] (protein.gro) (Optional)
61              Existing  configuration  to insert into: gro g96 pdb brk ent esp
62              tpr
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64       -ci [<.gro/.g96/…>] (insert.gro)
65              Configuration to insert: gro g96 pdb brk ent esp tpr
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67       -ip [<.dat>] (positions.dat) (Optional)
68              Predefined insertion trial positions
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70       -n [<.ndx>] (index.ndx) (Optional)
71              Extra index groups
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73       Options to specify output files:
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75       -o [<.gro/.g96/…>] (out.gro)
76              Output configuration after insertion: gro g96 pdb brk ent esp
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78       Other options:
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80       -replace <selection>
81              Atoms that can be removed if overlapping
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83       -sf <file>
84              Provide selections from files
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86       -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
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92       -box <vector> (0 0 0)
93              Box size (in nm)
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95       -nmol <int> (0)
96              Number of extra molecules to insert
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98       -try <int> (10)
99              Try inserting -nmol times -try times
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101       -seed <int> (0)
102              Random generator seed (0 means generate)
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104       -radius <real> (0.105)
105              Default van der Waals distance
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107       -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.
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112       -dr <vector> (0 0 0)
113              Allowed displacement in x/y/z from positions in -ip file
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115       -rot <enum> (xyz)
116              Rotate inserted molecules randomly: xyz, z, none
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SEE ALSO

119       gmx(1)
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121       More     information    about    GROMACS    is    available    at    <‐
122       http://www.gromacs.org/>.
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COPYRIGHT

125       2019, GROMACS development team
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1302019.2                           Apr 16, 2019          GMX-INSERT-MOLECULES(1)