[gmx-users] High speed performance

Asmaa El khodary asma.moh_990 at aucegypt.edu
Mon Aug 3 22:19:57 CEST 2015

Dr Carsten
Thank you so much for your reply. Yes, you are right, it's a 40 core CPU.
I'm using 2 fs time step with Particle Mesh Ewald for long-range
electrostatics. I've attached the parameter file I'm using for the
production run.
Best Regards

On Mon, Aug 3, 2015 at 4:03 PM, Asmaa El khodary <asma.moh_990 at aucegypt.edu>

> Hi,
> I'm currently simulating a protein consists of 2776 atoms with 173
> residues using CPU with 5 nodes, 40 core processors. The performance of the
> simulation is 70 ns per day (50 ns simulation takes almost 18 hours). Is
> this realistic or not?
> Thanks in Advance
> Asma

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