[gmx-users] (no subject)

Mark Abraham Mark.Abraham at anu.edu.au
Tue Dec 5 05:41:40 CET 2006

Bio wrote:
> Dear gmxns,
> HOpe u r enjoying the simulation.
> I have one trouble while executing a position restraint simulation to
> equilibrate for 100 ps for a protein ,it takes more time..I come to know
> that it is good if it takes not more than a day.......Eventhough I
> strictly followed the procedure,the PR simulation takes much time...It
> shows like....
> Getting Loaded...
> Reading file pr.tpr, VERSION 3.3.1 (single precision)
> Loaded with Money
> starting mdrun 'in water'
> 50000 steps,    100.0 ps.
> step 16830, will finish at Thu Dec  7 03:51:45 2006.
> Kindly suggest me what the possible ways to rectify the error.......... 

Position-restrained MD shouldn't take appreciably longer than MD without 
such restraints. Check that your .mdp file hasn't undergone any other 
changes, and that your computer system isn't more loaded.


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