gmx-insert-molecules(1) GROMACS Manual gmx-insert-molecules(1)NAMEgmx-insert-molecules - Insert molecules into existing vacancies
SYNOPSIS
gmx insert-molecules [-f [<.gro/.g96/...>]] [-ci [<.gro/.g96/...>]]
[-ip [<.dat>]] [-o [<.gro/.g96/...>]] [-nice <int>]
[-box <vector>] [-nmol <int>] [-try <int>] [-seed <int>]
[-radius <real>] [-scale <real>] [-dr <vector>]
[-rot <enum>] [-[no]allpair]
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.
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
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 data‐
base, 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 and output files:
-f [<.gro/.g96/...>] (protein.gro) (Input, Optional)
Structure file: gro g96 pdb brk ent esp tpr tpb tpa
-ci [<.gro/.g96/...>] (insert.gro) (Input)
Structure file: gro g96 pdb brk ent esp tpr tpb tpa
-ip [<.dat>] (positions.dat) (Input, Optional)
Generic data file
-o [<.gro/.g96/...>] (out.gro) (Output)
Structure file: gro g96 pdb brk ent esp
Other options:
-nice <int> (19)
Set the nicelevel
-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 den‐
sity 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
-[no]allpair (no)
Avoid momory leaks during neighbor searching with option -ci. May
be slow for large systems.
KNOWN ISSUES
- Molecules must be whole in the initial configurations.
- Many repeated neighbor searchings with -ci blows up the allocated
memory. Option -allpair avoids this using all-to-all distance checks
(slow for large systems)
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-insert-molecules(1)
