'\" t
.\"     Title: psize
.\"    Author: Manuel Prinz <debian@pinguinkiste.de>
.\" Generator: DocBook XSL Stylesheets vsnapshot <http://docbook.sf.net/>
.\"      Date: 2008-06-04
.\"    Manual: PDB2PQR Manual
.\"    Source: psize
.\"  Language: English
.\"
.TH "PSIZE" "1" "2008\-06\-04" "psize" "PDB2PQR Manual"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.\" http://bugs.debian.org/507673
.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\" -----------------------------------------------------------------
.\" * set default formatting
.\" -----------------------------------------------------------------
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.\" -----------------------------------------------------------------
.\" * MAIN CONTENT STARTS HERE *
.\" -----------------------------------------------------------------
.SH "NAME"
psize \- Get dimensions and other information from PQR files
.SH "SYNOPSIS"
.HP \w'\fBpsize\fR\ 'u
\fBpsize\fR [\fB\-\-cfact=\fR\fB\fIvalue\fR\fR] [\fB\-\-fadd=\fR\fB\fIvalue\fR\fR] [\fB\-\-space=\fR\fB\fIvalue\fR\fR] [\fB\-\-gememfac=\fR\fB\fIvalue\fR\fR] [\fB\-\-gememceil=\fR\fB\fIvalue\fR\fR] [\fB\-\-ofrac=\fR\fB\fIvalue\fR\fR] [\fB\-\-redfac=\fR\fB\fIvalue\fR\fR] {\fB\fIpqrfile\fR\fR}
.HP \w'\fBpsize\fR\ 'u
\fBpsize\fR {\fB\-\-help\fR | \fB\-h\fR}
.SH "DESCRIPTION"
.PP
\fBpsize\fR
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\&.
.PP
The calculation of this information can be influenced by giving constraints to
\fBpsize\fR
as parameters\&.
.SH "OPTIONS"
.PP
\fBpsize\fR
accepts the following options:
.PP
\fB\-\-help\fR, \fB\-h\fR
.RS 4
Print a help message and exit\&.
.RE
.PP
\fB\-\-cfact=\fR\fB\fIvalue\fR\fR
.RS 4
Factor by which to expand the molecule dimensions to get the coarse grid dimensions
.RE
.PP
\fB\-\-fadd=\fR\fB\fIvalue\fR\fR
.RS 4
Amount to add to the molecule dimensions to get the fine grid dimensions\&.
.RE
.PP
\fB\-\-space=\fR\fB\fIvalue\fR\fR
.RS 4
Desired fine mesh resolution\&.
.RE
.PP
\fB\-\-gememfac=\fR\fB\fIvalue\fR\fR
.RS 4
Number of bytes per grid point required for sequential
MG
calculation\&.
.RE
.PP
\fB\-\-gememceil=\fR\fB\fIvalue\fR\fR
.RS 4
Maximum
MB
allowed for sequential
MG
calculation\&. Adjust this to force the script to perform faster calculations (which require more parallelism)\&.
.RE
.PP
\fB\-\-ofrac=\fR\fB\fIvalue\fR\fR
.RS 4
Overlap factor between mesh partitions\&.
.RE
.PP
\fB\-\-redfac=\fR\fB\fIvalue\fR\fR
.RS 4
Maximum factor by which a domain dimension can be reduced during focusing\&.
.RE
.SH "SEE ALSO"
.PP
\fBapbs\fR(1),
\fBpdb2pqr\fR(1)
.SH "AUTHOR"
.PP
\fBManuel Prinz\fR <\&debian@pinguinkiste\&.de\&>
.RS 4
Wrote this manpage for the Debian System\&.
.RE
.SH "COPYRIGHT"
.br
Copyright \(co 2008 Manuel Prinz
.br