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

Szilárd Páll pall.szilard at gmail.com
Fri May 2 17:25:57 CEST 2014


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:
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",

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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