[gmx-users] energy minimization problem

[Justin Lemkul]

On 5/14/15 3:12 AM, Ming Tang wrote:
> Dear all,
>
> I am working with a triple helix containing around 1000 amino acids per chain using martini force field. After energy minimization until it cannot be minimized any more, I moved to NPT, but got LINCS error after thousands of steps. Following Justin's advice on LINCS error, I checked all of the possible causes in blowing up page, but still did not find the reason. Later, I created a smaller model including 30 amino acids per chain, and found it could be move forward to dynamic simulation smoothly using the same control files. Does this mean that my control files are ok?
> I noticed that the minimization was not good enough when working with my real triple helix, as it got stuck in a certain atom (Epot does not change). I have tried to change to use cg algorithm, but got no improvement. Could anybody tell me how to further minimize my triple helix. I got stuck here for 3 days.
>

Sounds like your initial geometry is just bad.  Inspect the surroundings of the 
atom with maximum force; that usually gives an indication of what's going on.

-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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