[gmx-users] Nano-structures equilibration

[Mohammad Roostaie]

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 GROMACSwebsite 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 onexactly 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
>