[gmx-users] Nano-structures equilibration

[Alex]

You have performance-related errors, maybe try a different number of 
ranks, or another machine, or OpenMP instead of MPI -- hope others will 
be able to comment on technical issues.
Your question was whether you should abandon nanostructure equilibration 
because of this -- the answer is of course no.

Alex


On 6/30/2017 5:03 AM, Mohammad Roostaie wrote:
> I asked it since I got some errors regarding the NPT equilibration, 
> also this link says that turn off the pressure coupling.
>
> The errors which I received is as follow:
>
> Fatal error:
> The number of ranks you selected (14) contains a large prime factor 7. 
> In most cases this will lead to bad performance. Choose a number with 
> smaller prime factors or set the decomposition (option -dd) manually.
> For more information and tips for troubleshooting, please check the 
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> —---------------------------------------------------—
>
> Halting parallel program mdrun_mpi on rank 0 out of 14
> —------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
>
> Furthermore, I used -dd (with the values of 7 2 1) option, and I got 
> this error:
>
> Fatal error:
> 1130 particles communicated to PME rank 14 are more than 2/3 times the 
> cut-off out of the domain decomposition cell of their charge group in 
> dimension y.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the 
> GROMACS
> website at Errors - Gromacs
>
> Regards,
> M
>
> ------------------------------------------------------------------------
> On Friday, June 30, 2017, 12:47:05 PM GMT+4:30, Alex 
> <nedomacho at gmail.com> wrote:
>
>
> Is this a philosophical question? Yes, it is certainly possible for
> graphene+peptide to exist in water under pressure.
>
>
> On 6/30/2017 12:05 AM, Mohammad Roostaie wrote:
> > Hi All,
> > Is it possible and necessary to run NPT equilibration process on the 
> nanostructure systems (graphene+peptide in water)? Since I got some 
> errors regarding this process.
> > Regards,Mohammad
> >
>