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

[Szilárd Páll]

PS: Perhaps we should simply suggest to use no DD and OpenMP
parallelization only?

--
Szilárd


On Fri, May 2, 2014 at 5:57 PM, Szilárd Páll <pall.szilard at gmail.com> wrote:

> 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
>>
>> --
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>
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