[gmx-users] Imidazolium ring opening during energy minimization

[Justin Lemkul]

On 2/19/15 2:21 AM, Meena Singh wrote:
> Dear GROMACS users,
>
> I am trying to simulate box of 1-ethyl-3-methylimidazolium ion (5-membered
> ring with overall +1 charge) with its counter ion tetrafluoroborate.
> I am using OPLS forcefield.
> Partial charges and potential parameters have been taken from research
> paper.
> But during energy minimization 5-membered ring of all molecules of
> imidazolium ion  is getting opened by breaking a bond between N (attached
> to ethyl group in ring) and C (attached to other C in ring)
>
>
> Does anyone have a suggestion to help me with this problem?
>

Bonds can't break in classical MD or energy minimization.  Either your topology 
or initial coordinates have something wrong with it and you're seeing distortion 
as a result ("broken" bonds in visualization software are due to the heuristic 
algorithms that software uses, and is not an indication that a bond has actually 
broken).

-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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