[gmx-users] fatal error with mpi

[Stefano Guglielmo]

Dear users,

I have installed gromacs with MPI instead of its native tMPI and I am
encountering the following error:
"Fatal error:
4 particles communicated to PME rank 5 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."

I am using 8 MPI ranks with 4 omp threads per rank (it was the
configuration used on the same machine by tMPI), but I also tried 4 ranks
with 8 threads, but it did not solve the problem.

I don't think this is an issue related to my system because the same system
run with the native tMPI works properly (it has already been termalized and
gradually equilibrated); neverthless I tried to reduce dt and temperature
but without any benefit. Does anybody have any suggestions?

Thanks in advance
Stefano

-- 
Stefano GUGLIELMO PhD
Assistant Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707178