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

hess@kth.se hess at kth.se
Fri May 2 17:37:10 CEST 2014

Since with the Verlet scheme charge groups are single atoms, this error is correct. But some more explanation could be useful.



----- 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

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.

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