gmx insert-molecules¶
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:
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