On 4/25/12 10:49 AM, Albert wrote:
hello Justin:
thank you very much for your such kind explanations. It is quite helpful.
I am wondering how many CPU did you usually use for the membrane simulations?
and how many ns/day can you get the best if CPU is not a problem with Gromacs? I
am very confused about this question since some one claimed that they can use
optimized PMF/F paramters to achieve even 100ns/day for 20,000 atoms system. I
also try to use g_tune_pme to get a better performance, but the results are not
so satisfied...... Can you give me some advices for this?
I have never been able to get anywhere close to such performance for explicit
solvent calculations using PME. Maybe others who have can describe their
experience. I don't have an exact benchmark for the tutorial runs, but 24 CPU's
gave somewhere in the ballpark of 10-15 ns/day on our (relatively old) hardware.
My rule of thumb is 1000 atoms/CPU, and then tweak from there if necessary.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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