[gmx-users] Re: equilibrium stage runs for too long

Dr. Vitaly Chaban vvchaban at gmail.com
Thu Aug 23 22:45:51 CEST 2012

> Dear all,
> I'm performing NVT on a system consisting a water layer, a decane layer
> and a lipid layer in between those two layers. There are 40 lipids, 627
> decane molecules and 8577 water molecules in total.
> The EM was conducted successfully, however, when I try to run NVT on
> this system, it seems to take forever. I'm using 48 cores on a super
> computer and the report suggests it has token 367 hours already for the
> performance of one core, and it still has not finished yet.
> So I'm wondering does it really require so much time to run or is there
> something wrong in my system which prevents it to converge?
> Additionally, there's a running time specified in the mdp file which in
> my case is 100 ps, so I suppose the simulation should end when the time
> limit is reached regardless of whether the pressure converges to the
> reference value?
> I'm new to gromacs, could anyone help me with this? Your efforts are
> very much appreciated!
> Thanks a lot!

Dear Clare -

I believe there is a problem with your particular run. Your system
should sample its 100ps for one day even using just one processor.
Please, look at your MD.LOG file and report it here.


Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216

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