On 29/03/2012 11:03 AM, Dr. Vitaly V. Chaban wrote:
I am using gromacs for membrane simulation (under CHARMM36 FF) which
contains around 80,000 atoms. I've submitted over 200 CPU in the cluster
for such system with 2 fs time step. And what really astonished is that the
efficiency for such simulation is only 3ns/day..... I am wondering what
happen to my system or gromacs? What can I do to fasten the simulation?
here is my md.mdp:
*
title = god!
cpp = /usr/bin/cpp
include =
define =
integrator = md
dt = 0.001
nsteps = 100000000
nstxout = 1000000
nstvout = 1000000
nstlog = 1000000
nstenergy = 10000
nstxtcout = 100000
xtc_grps =
energygrps = Protein POPC SOL ION
nstcalcenergy = 1
I agree with the other thoughts mentioned, and would add that
nstcalcenergy = 1 triggers global communication every integration step,
and that is increasingly inefficient at high parallelization.
Mark
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