This is the command gmx-insert-molecules that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
gmx-insert-molecules - Insert molecules into existing vacancies
SYNOPSIS
gmx insert-molecules [-f [<.gro/.g96/...>]] [-ci [<.gro/.g96/...>]]
[-ip [<.dat>]] [-o [<.gro/.g96/...>]] [-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
discarded.
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, thoseatoms are assigned the
(pre-scaled) distance -radius.
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
Options to specify output files:
-o [<.gro/.g96/...>] (out.gro)
Output configuration after insertion: gro g96 pdb brk ent esp
Other options:
-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> (1997)
Random generator seed
-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>
Rotate inserted molecules randomly: xyz, z, none
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