[gmx-users] NPT error

[Mohammad Roostaie]

Hi,
I tried -dd option with (7 2 1) value and 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

I passed the NVT process with "-dd 7 2 1" option. Actually, I modeled graphene and protein in water. Is it necessary to run NPT equilibrium on this nano-system? 


      From: ‪Mohammad Roostaie‬ ‪ <mohammad.r0325 at yahoo.com>
 To: Discussion List for GROMACS Users <gmx-users at gromacs.org> 
 Sent: Monday, 26 June 2017, 9:12:05
 Subject: NPT error
  
Hi All, I wanted to perform NPT equilibration, but I got this error: 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. 
I performed energy minimization and NVT successfully, and the final energy level was 30864982016.000000 kJ/molCan you please help me figure this out? If you need further information please let me know.
Regards,Mohammad