[gmx-users] infinite polymer crystals at gromacs 4.x.x
gmx3 at hotmail.com
Mon Feb 2 10:08:55 CET 2009
pbc=full is replaced by the mdp option periodic_molecules,
which works both with pbc=xyz and pbc=xy.
> 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.
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