[gmx-users] CPU usage
feenstra at chem.vu.nl
Tue Jun 8 18:09:10 CEST 2004
Christopher Tran wrote:
> Quoting F Jiang <jiangf at aphy.iphy.ac.cn>:
>>Also, what's the MD running time for a protein of 100aa in water (-d 0.5 box)
>>or 10 steps?
> This depends on your CPU, the values you have set for dt and nsteps, and many
> other factors. The best thing to do is to use the -v flag when you use the
> MDRUN command to see the approximate finishing time.
Ten steps for 100aa + water should not take more than a few minutes (execpt
mayb if you still have very old hardware ... ;-). -d 0.5 is a bit small box,
though, since with a normal 0.8/1.4 cut-off this would mean the protein
could interact with itself over the periodic boundary.
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