[gmx-users] reasons for slow computation?

Yun Shi yunshi09 at gmail.com
Mon Oct 10 21:10:56 CEST 2011

Hi all,

I am doing MD simulation on two almost identical protein-ligand systems with
GROMACS4.5.4 and amber99SB force fields.

Almost every single parameter I used for this two systems are the same (I
literally copied the mdp files for both), except that one has 65235 atoms
while the other has 65205 atoms, which is caused by the difference of 10
water molecules.

However, the 65235-atom one is significantly slower than the 65205-atom one,
the computational speed (performance) ratio is roughly 1:3.

I am really confused, since the only differences between them that I can
think of are:

1. The configuration of ligands, that is, alpha sugar vs beta sugar
2. number of water molecules, 19477 vs 19467
3. octahedral box size, ~726.119 nm^3 vs ~726.322 nm^3
4. probably the initial velocities, since I am used gen_seed    = -1
5. the cpu specs, as I am using a cluster (I specified procs=72 for both
system and I assume they were assigned to different cpus randomly), which
consists of Intel Xeon E5450 quad-core processor, running at 3.0 GHz, and
Intel Xeon X5650 6-core processors running at 2.67 GHz

How come the performance could have a 1:3 difference?

Thanks for any suggestion!
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