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Full Discussion: ps command
Top Forums UNIX for Dummies Questions & Answers ps command Post 302644575 by muffle on Tuesday 22nd of May 2012 06:58:00 AM
Old 05-22-2012
Thanks to both jlliagre & radoulov. I understand now.
 

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genconf(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					genconf(1)

NAME
genconf - multiplies a conformation in 'random' orientations VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
genconf -f conf.gro -o out.gro -trj traj.xtc -[no]h -[no]version -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 etc. -o out.gro Output Structure file: gro g96 pdb etc. -trj traj.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno Print version 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 180 180 180 Maximum random rotation -[no]renumberyes Renumber residues KNOWN PROBLEMS
- The program should allow for random displacement of lattice points. SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 genconf(1)
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