[gmx-developers] strange SHAKE + Verlet scheme warning?

[Szilárd Páll]

I see. So that means that SHAKE is even more useless and DD will work only
if the domains is empty?

--
Szilárd


On Fri, May 2, 2014 at 5:37 PM, hess at kth.se <hess at kth.se> wrote:

> Hi,
>
> Since with the Verlet scheme charge groups are single atoms, this error is
> correct. But some more explanation could be useful.
>
> Cheers,
>
> Berk
>
> ----- Reply message -----
> From: "Szilárd Páll" <pall.szilard at gmail.com>
> To: "Discussion list for GROMACS development" <gmx-developers at gromacs.org>
> Subject: [gmx-developers] strange SHAKE + Verlet scheme warning?
> Date: Fri, May 2, 2014 17:25
>
> Hi,
>
> I've come across a somewhat strange issue and I thought I'd ask before
> filing a redmine - especially as I'm not sure whether this is only a
> documentation/code self-documentation bug or a buggy behavior too.
>
> I'm running 5.0 RC1 (git), Verlet scheme with a small water box of ~500
> molecules and -DFLEXIBLE with SHAKE constraints.
>
> Trying to start a DD run I get this error:
>
> -------------------------------------------------------
> Program mdrun_d, VERSION 5.0-rc1-dev-20140430-81378bd
> Source code file:
> /home/pszilard/projects/gromacs/gromacs-5.0/src/gromacs/mdlib/constr.c,
> line: 1266
>
> Fatal error:
> SHAKE is not supported with domain decomposition and constraint that cross
> charge group boundaries, use LINCS
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> Now, this is inconsistent at least with the fact that charge groups are
> removed by grompp with the Verlet scheme. The documentation does point out
> that "SHAKE does not support constraints between atoms on different nodes",
> though.
>
> Looking a the code, the bInterCGcons that triggers it still refers to
> charge groups, so there is definitely room for improvement both in error
> message, variable naming, as well as documentation.
>
> Cheers,
> --
> Szilárd
>
> --
> Gromacs Developers mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developersor send a mail to
> gmx-developers-request at gromacs.org.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20140502/32ae751a/attachment.html>