PSIZE(1) PDB2PQR Manual PSIZE(1)NAME
psize - Get dimensions and other information from PQR files
SYNOPSIS
psize [--cfact=value] [--fadd=value] [--space=value] [--gememfac=value] [--gememceil=value] [--ofrac=value] [--redfac=value] {pqrfile}
psize {--help | -h}
DESCRIPTION
psize derives information from PQR files to preprare the models of proteins and chemicals for electrostatics calculations. The tool
calculates dimensions for coarse and fine grids, grid spacings, box size and estimates the memory required to perform an electrostatics
calculation.
The calculation of this information can be influenced by giving constraints to psize as parameters.
OPTIONS
psize accepts the following options:
--help, -h
Print a help message and exit.
--cfact=value
Factor by which to expand the molecule dimensions to get the coarse grid dimensions
--fadd=value
Amount to add to the molecule dimensions to get the fine grid dimensions.
--space=value
Desired fine mesh resolution.
--gememfac=value
Number of bytes per grid point required for sequential MG calculation.
--gememceil=value
Maximum MB allowed for sequential MG calculation. Adjust this to force the script to perform faster calculations (which require more
parallelism).
--ofrac=value
Overlap factor between mesh partitions.
--redfac=value
Maximum factor by which a domain dimension can be reduced during focusing.
SEE ALSO apbs(1), pdb2pqr(1)AUTHOR
Manuel Prinz <debian@pinguinkiste.de>
Wrote this manpage for the Debian System.
COPYRIGHT
Copyright (C) 2008 Manuel Prinz
psize 2008-06-04 PSIZE(1)
Check Out this Related Man Page
gmk_hy(1) Scotch user's manual gmk_hy(1)NAME
gmk_hy, gmk_m2, gmk_m3, gmk_ub2 - create source graphs
SYNOPSIS
gmk_hy [options] dim [ofile]
gmk_m2 [options] [-gcfile] dimX dimY [ofile]
gmk_m3 [options] [-gcfile] dimX dimY dimZ [ofile]
gmk_ub2 [options] dim
DESCRIPTION
The gmk_* programs create source graph files for some common, regular topologies.
gmk_hy creates a hypercube of dimension dim.
gmk_m2 creates a 2D regular grid of dimensions dimX and dimY.
gmk_m3 creates a 3D regular grid of dimensions dimX, dimY and dimZ.
gmk_ub2 creates an unoriented de Bruijn graph of dimension dim.
OPTIONS -b base
For gmk_m2 and gmk_m3 only. Output graphs with base value set to base. Default value is 0.
-e For gmk_m2 only. Build a 8-neighbor grid rather than a 4-neighbor grid.
-gcfile
For gmk_m2 and gmk_m3 only. Output graph vertex coordinates (that is, geometry data to be used by gout(1)) in file cfile.
-h Display some help.
-t For gmk_m2 and gmk_m3 only. Create torus graphs, that is, graphs such that there exist loop edges between vertices of rank 0 and
(dim-1) in every dimension.
-V Display program version and copyright.
EXAMPLE
Create a 5x7 grid along with its geometry:
$ gmk_m2 5 7 -g/tmp/m5x7.xyz /tmp/m5x7.grf
SEE ALSO gbase(1), gmk_msh(1), gtst(1), gmap(1), gord(1), gout(1), amk_grf(1).
Scotch user's manual.
AUTHOR
Francois Pellegrini <francois.pellegrini@labri.fr>
February 14, 2011 gmk_hy(1)
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