[gmx-users] energy minimization problem

[Justin Lemkul]

On 6/1/15 9:07 AM, soumadwip ghosh wrote:
> Hi Justin,
>              the snapshot I uploaded in the URL is of the SSDNA-CNT
> system after energy minimization step not before it. I stripped off
> water and ions from the system for the ease of visualization. I would
> be grateful if you suggest me a possible way out.
>

I don't see how that changes what I've said.  You have a topology problem with 
the CNT.  Simplify the system - build a smaller CNT, minimize it in vacuo, etc, 
then make it bigger/more complex.  Look at the atoms that are distorting and 
check the existence of their bonded interactions and associated parameters.

-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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