[gmx-users] infinite polymer crystals at gromacs 4.x.x

David van der Spoel spoel at xray.bmc.uu.se
Sun Feb 1 17:45:13 CET 2009

Claus Valka wrote:
> Hello,
> back in gromacs versions 3.x.x there was the ability to simulate 
> (polymer) crystals by enabling the option pbc = full in the mdp file.
> That way someone was avoiding the inconsistent shifts message and was 
> able to simulate infinite systems.
> My question is: now in gromacs versions 4.0 and on, is this feature 
> abandoned? 
> The screw option, which is new, I do not think that replaces the full 
> option. The full option is no longer selectable. Is there any other way? 
> Or in order to use the files we were using we have to stick with older 
> versions?

It should work by default in 4.0 using pbc=xyz, at least in mdrun. Let 
us know if there are problems with other tools.
> Yours Sincerely,
> Nikos
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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