NAME
genconf - multiplies a conformation in ’random’ orientations
VERSION 4.0.1
SYNOPSIS
genconf -f conf.gro -o out.gro -trj traj.xtc -[no]h -nice int -nbox
vector -dist vector -seed int -[no]rot -[no]shuffle -[no]sort -block
int -nmolat int -maxrot vector -[no]renumber
DESCRIPTION
genconf multiplies a given coordinate file by simply stacking them on
top of each other, like a small child playing with wooden blocks. The
program makes a grid of user defined proportions ( -nbox), and
interspaces the grid point with an extra space -dist.
When option -rot is used the program does not check for overlap
between molecules on grid points. It is recommended to make the box in
the input file at least as big as the coordinates + Van der Waals
radius.
If the optional trajectory file is given, conformations are not
generated, but read from this file and translated appropriately to
build the grid.
FILES
-f conf.gro Input
Structure file: gro g96 pdb tpr tpb tpa
-o out.gro Output
Structure file: gro g96 pdb
-trj traj.xtc Input, Opt.
Trajectory: xtc trr trj gro g96 pdb cpt
OTHER OPTIONS
-[no]hno
Print help info and quit
-nice int 0
Set the nicelevel
-nbox vector 1 1 1
Number of boxes
-dist vector 0 0 0
Distance between boxes
-seed int 0
Random generator seed, if 0 generated from the time
-[no]rotno
Randomly rotate conformations
-[no]shuffleno
Random shuffling of molecules
-[no]sortno
Sort molecules on X coord
-block int 1
Divide the box in blocks on this number of cpus
-nmolat int 3
Number of atoms per molecule, assumed to start from 0. If you set this
wrong, it will screw up your system!
-maxrot vector 90 90 90
Maximum random rotation
-[no]renumberyes
Renumber residues
KNOWN PROBLEMS
- The program should allow for random displacement off lattice points.
SEE ALSO
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 genconf(1)