[gmx-users] MARTINI crushing
p.c.kroon at rug.nl
Thu Apr 14 09:40:20 CEST 2016
1) use a newer version of Gromacs
2) try passing -rdd 1.4 or even 1.6 to mdrun. The bonds in Elnedyn are so
long and flexible they occasionally confuse gromacs' domain decomposition.
On Thu, Apr 14, 2016 at 8:49 AM, James Starlight <jmsstarlight at gmail.com>
> Dear Gromacs Users!
> I faced with the problems while simulating of big MARTINI system of
> membrane protein complex within big membrane consisted totally of 55k
> martini CG atoms.
> On the early stage of the NPT equilibration I have a error
> Program g_mdrun_openmpi, VERSION 4.5.7
> Source code file:
> /builddir/build/BUILD/gromacs-4.5.7/src/mdlib/domdec_top.c, line: 173
> Software inconsistency error:
> Some interactions seem to be assigned multiple times
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> does the problem is related to paralelization or smth wrong with
> setup? Amazing that on the same system without Elnedyn applied I have
> no such promlems at ell.
> Thanks so much for help!
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