[gmx-developers] pdb2gmx, -water option, and non-standard models

Daniel Larsson larsson at xray.bmc.uu.se
Fri Apr 15 11:37:09 CEST 2011

An easy solution to "choose" the water model is to just edit the output from pdb2gmx.

sed -i 's#amber99sb-ildn.ff/tip3p.itp#/path/to/custom/topology/tip4pew.itp#' topol.top


On Apr 14, 2011, at 19:43 , Joshua L. Phillips wrote:

> Hi All,
> pdb2gmx is a great tool and I really like the flexibility to specify
> different forcefields using the -ff option (great for scripting)!
> However, when selecting water models, I was recently disappointed that
> the water selection option (-water) was an enumeration because it lacks
> the flexibility to test novel water models. For instance, even a highly
> regarded model like "tip4pew" isn't specified in the enumeration.
> Maybe the -water option could be changed to a string (similar to -ff) in
> order to allow easy selection of "non-standard" water models? I am not
> familiar with the technical issues that might need to be addressed, so
> this is just a humble suggestion.
> Thanks!
> -- 
> Joshua L. Phillips
> Ph.D. Candidate
> School of Engineering
> University of California, Merced
> Email: jphillips7 at ucmerced.edu
> Phone: (209) 723-0921
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