[gmx-users] Speeding up simulation

sapna sarupria sapna.sarupria at gmail.com
Tue Aug 17 21:38:20 CEST 2010

Hi all,

I am running (NVT) simulations of a drop of water (~5 nm in radius) in a big
box (~25 nm) in a box and find that the simulations are rather slow. I am
getting about 0.8 ns per day when a simulation of bulk system of equivalent
number of waters will be much faster. The number of waters is ~12000. I was
wondering if anyone can suggest methods with which I can speed up the
simulations. I am using domain decomposition and optimize_fft is set to yes.
PME is used for the electrostatics.

Thank you

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