[gmx-users] remd

[Justin Lemkul]

On 7/8/13 11:13 AM, Shine A wrote:
> Sir,
>
>     I did an REMD for a peptide using implicit solvent model(8 replica 10 ns
> each).The experimental structure of peptide in water look like
> betasheet(from circular dichroism). But almost all conformations  from
> trajectory look like alpha-helices.Then how I can correlate experimental
> and theoretical results.
>

Structural features are largely determined by the force field you've chosen to 
use.  Some have intrinsic biases that are usually well described in the literature.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Associate

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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