[gmx-users] MARTINI crushing

[James Starlight]

an question: might the bigger -rdd like 1.8 or 2.0  produce ssmth bad
in simulation? generally I found that with rdd 1.8 the siduation is
better, also I reduced number of CPU for that job from 256 to 128 and
it works OK by now!

Gleb

2016-04-14 9:40 GMT+02:00 Kroon, P.C. <p.c.kroon at rug.nl>:
> Hi James,
>
> 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.
>
> Peter
>
> On Thu, Apr 14, 2016 at 8:49 AM, James Starlight <jmsstarlight at gmail.com>
> wrote:
>
>> 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!
>>
>> J.
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