[gmx-users] domain decomposition error

Mark Abraham mark.j.abraham at gmail.com
Mon Jun 18 09:29:53 CEST 2018


The implicit solvent support got a bit broken between 4.5 and 4.6, and
nobody has yet worked out how to fix it, sorry. If you can run with 1 cpu,
do that. Otherwise, please use GROMACS 4.5.7.


On Mon, Jun 18, 2018 at 9:21 AM Chhaya Singh <chhayasingh014 at gmail.com>

> I am running a simulation having protein in implicit solvent using amber
> ff99sb forcefield and gbsa as solvent .
> I am not able to use more than one cpu.
> It always gives domain decomposition error if i use more than one cpu.
> when i tried running using one cpu then it gave me this error :
> "Fatal error:
> Too many LINCS warnings (12766)
> If you know what you are doing you can adjust the lincs warning threshold
> in your mdp file
> or set the environment variable GMX_MAXCONSTRWARN to -1,
> but normally it is better to fix the problem".
> --
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