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Dear Gromacs users
During simulating DPPC membrane I confront with several Problems. I
intend to express them here and I really appreciate it if you help me.
Briefly I started to simulate a DPPC containing 2000 W and 128 DPPC
molecules. the trend ( I mean the way it increase or decrease) of
Pressure xx is important to me. as one can expect, due to the size of my
system ( number of atom) the result is so erratic� ( about 200bar).
so I enlarge the system in X-direction considering consistent trend for
both system. so I replicated system in X-direction, minimized it and do
an NPT on it.
during NPT, my working job blew up with this error :
An atom moved too far between two domain decomposition steps
does this error relate to the number of cpu-cores, because when I
decrease number of the cores from 16 to 8 using -nb 8, I don't see
this error again, but there is no progress in the number of steps !!!
also I have question about MPI. In my laptop when I simulate a box ( 128
DPPC with 2000 W), the system runs with :
Using 1 MPI thread
Using 4 OpenMP threads
when I do the same, in High performance Computer of the university, Its
output is totally different which also uses automatically :
Using 24 MPI threads
Using 1 OpenMP thread per tMPI thread
but when I used -ntmpi 1 to change MPI threads to 1, it gave the same
answer as my laptop. so what is the optimum number of -ntmpi and -nt ?! I
should notice that I now what is the meaning of MPI and thread, but
don't now what is the optimum number !!!!
best� regards
Ali
==================
Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)
Department of Mechanical Engineering
Sharif University of Technology, Tehran, Iran
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