[gmx-users] Re: gmx-users Digest, Vol 48, Issue 24

Bert bert.ustc at gmail.com
Sat Apr 12 21:50:22 CEST 2008


Thanks David. There still "inconsitent shifts" warnings with a tpr made by
pbc=xyz. By the way, my itp file is not changed, that is, the bonded
terms between periodic images  are still in the topology. Should I make a
topology with pbc=xyz too?

>
> Bert wrote:
> > Hi all,
> >
> > I use pbc=full in my system, and all runs are ok except for the
> > "inconsistent shifts" warnings when I use some analysis tools, such as
> > g_density, g_densmap, etc. I have searched the whole list related to
> > this problem, and I doubt several analysis tools are not coded with
> > consideration of full pbc. Am I right? If so, how to deal with these
> > warnings? Thanks in advance.
>
> make a tpr with pbc=xyz for analysis.
> >
> >
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>
> --
> David van der Spoel, Ph.D.
> 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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