[gmx-users] CG MD

[Justin Lemkul]

On 6/23/17 10:26 AM, Alex Mathew wrote:
> Dear all,
> I was wondering the analysis we usually use in the all-atom simulation will
> work in for CG model?
> I guess secondary structural analysis will be useless since it's not
> considering all atoms. What about non-bonded energies and other parameters
> such hydrogen bond and essential dynamics?

What do people do in the literature to address the same types of questions 
you're asking.  H-bonding is a microscopic property and likely is not going to 
be addressed via CG, though most atomistic properties can be studied by 
rebuilding the atomistic coordinates from the CG.  Various methods exist to do this.

-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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