[gmx-users] Re: generating user-defined topologies for surfaces

[Justin Lemkul]

On 7/30/13 9:58 AM, Valentina wrote:
> A follow up question  - does searching for neighbouring atoms to bond to
> according to specbond.dat slow down calculation and if so how significantly.
>

I've never seen specbond.dat affect pdb2gmx by more than a few seconds, but it 
depends on the size of the structure.  Only one way to find out...

-Justin

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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