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gmx insert-molecules |
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| Main Table of Contents | VERSION 5.0.2 | |
gmx insert-molecules [-f [<.gro/.g96/...>]] [-ci [<.gro/.g96/...>]]
[-ip [<.dat>]] [-o [<.gro/.g96/...>]] [-nice ]
[-box ] [-nmol ] [-try ] [-seed ]
[-radius ] [-scale ] [-dr ] [-rot ]
[-[no]allpair]
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).