genconf VERSION 3.3_beta_20050823

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

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.

-f conf.gro Input Generic structure: gro g96 pdb tpr tpb tpa xml

-o out.gro Output Generic structure: gro g96 pdb xml

-trj traj.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb

-[no]h no 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]rot no Randomly rotate conformations

-[no]shuffle no Random shuffling of molecules

-[no]sort no 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]renumber yes Renumber residues

- The program should allow for random displacement off lattice points.

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.