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

[Bert]

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.
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> --
> 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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080413/56aecd6a/attachment.html>