[gmx-users] CPU usage

[Anton Feenstra]

Christopher Tran wrote:

> Quoting F Jiang <jiangf at aphy.iphy.ac.cn>:
> 
> 
>>Dear All,
>>
>> 
>>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.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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