[gmx-users] CPU usage

Anton Feenstra 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>:
> 
> 
>>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 |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




More information about the gromacs.org_gmx-users mailing list