1 .TH genconf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
3 genconf - multiplies a conformation in 'random' orientations
5 .B VERSION 4.5.4-dev-20110404-bc5695c
10 .BI "\-trj" " traj.xtc "
12 .BI "\-[no]version" ""
14 .BI "\-nbox" " vector "
15 .BI "\-dist" " vector "
18 .BI "\-[no]shuffle" ""
21 .BI "\-nmolat" " int "
22 .BI "\-maxrot" " vector "
23 .BI "\-[no]renumber" ""
25 \&\fB genconf\fR multiplies a given coordinate file by simply stacking them
26 \&on top of each other, like a small child playing with wooden blocks.
27 \&The program makes a grid of \fI user\-defined\fR
28 \&proportions (\fB \-nbox\fR),
29 \&and interspaces the grid point with an extra space \fB \-dist\fR.
32 \&When option \fB \-rot\fR is used the program does not check for overlap
33 \&between molecules on grid points. It is recommended to make the box in
34 \&the input file at least as big as the coordinates +
35 \&van der Waals radius.
38 \&If the optional trajectory file is given, conformations are not
39 \&generated, but read from this file and translated appropriately to
44 Structure file: gro g96 pdb tpr etc.
48 Structure file: gro g96 pdb etc.
50 .BI "\-trj" " traj.xtc"
52 Trajectory: xtc trr trj gro g96 pdb cpt
56 Print help info and quit
58 .BI "\-[no]version" "no "
59 Print version info and quit
61 .BI "\-nice" " int" " 0"
64 .BI "\-nbox" " vector" " 1 1 1"
67 .BI "\-dist" " vector" " 0 0 0"
68 Distance between boxes
70 .BI "\-seed" " int" " 0"
71 Random generator seed, if 0 generated from the time
74 Randomly rotate conformations
76 .BI "\-[no]shuffle" "no "
77 Random shuffling of molecules
79 .BI "\-[no]sort" "no "
80 Sort molecules on X coord
82 .BI "\-block" " int" " 1"
83 Divide the box in blocks on this number of cpus
85 .BI "\-nmolat" " int" " 3"
86 Number of atoms per molecule, assumed to start from 0. If you set this wrong, it will screw up your system!
88 .BI "\-maxrot" " vector" " 180 180 180"
89 Maximum random rotation
91 .BI "\-[no]renumber" "yes "
95 \- The program should allow for random displacement of lattice points.
100 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.