[gmx-users] equilibrium stage runs for too long

Clare evenstar32 at gmail.com
Thu Aug 23 19:20:11 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!


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