[gmx-users] Is it possible to turn off protein-water interaction?
feenstra at chem.vu.nl
Thu May 22 08:55:01 CEST 2003
Ruhong Zhou wrote:
> Dear David and Eirk,
> Thanks for the suggestions and comments. I guess to extend the
> non-bonded energy exclusion list and add some kind of volume-repulsion
> term might be a good idea in general, however, some extra coding and
> manipulation to the rtp files seem necessary. So I will think about
> other alternatives and then decide what to do. Maybe Erik will have
> something ready soon.
If you want to keep things as simple as possible, to start with, you
should focus on the .top file, which means that you don't have to modify
pdb2gmx (there is a lot of topology magic in that code you don't want
to know about), but you 'only' have to worry about grompp and mdrun,
which are much more structured and ordered in their design and coding.
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| _ _ ___,| K. Anton Feenstra |
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