psize(1) Get dimensions and other information from PQR files


psize [--cfact=value] [--fadd=value] [--space=value] [--gememfac=value] [--gememceil=value] [--ofrac=value] [--redfac=value] {pqrfile}
psize {--help | -h}



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.


psize accepts the following options:

--help, -h

Print a help message and exit.


Factor by which to expand the molecule dimensions to get the coarse grid dimensions


Amount to add to the molecule dimensions to get the fine grid dimensions.


Desired fine mesh resolution.


Number of bytes per grid point required for sequential MG calculation.


Maximum MB allowed for sequential MG calculation. Adjust this to force the script to perform faster calculations (which require more parallelism).


Overlap factor between mesh partitions.


Maximum factor by which a domain dimension can be reduced during focusing.


Manuel Prinz <[email protected]>

Wrote this manpage for the Debian System.


Copyright © 2008 Manuel Prinz