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

[Berk Hess]

Hi,

pbc=full is replaced by the mdp option periodic_molecules,
which works both with pbc=xyz and pbc=xy.

Berk

> Date: Sun, 1 Feb 2009 17:45:13 +0100
> From: spoel at xray.bmc.uu.se
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] infinite polymer crystals at gromacs 4.x.x
> 
> 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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