[gmx-users] bad contacts on lipid tails

[Justin Lemkul]

On 6/14/17 5:23 PM, Mohsen Ramezanpour wrote:
> I have done equilibration for almost 45 ns or even 60 ns for one test
> system.
> 
> I expected with this energy and this equilibration time, it works fine. But
> it fails.
> 
> I will construct the systems as you suggested to see what I get.
> 

With such a long equilibration, there's no reason it should fail with dt = 2 fs 
if the clashes have been eliminated, because I would expect they should be gone 
after a few ps.  I'd suspect something else in the topology or .mdp file but 
you'll have to do a more thorough diagnosis (e.g. 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System)

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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