[gmx-users] peptide aggregation

[Justin Lemkul]

On 2/11/14, 1:59 PM, Shine A wrote:
> Hi,
>
>         Now I am studying the aggregation propensity of a peptide using
> gromacs. To study the effect of neighbouring molecules on aggregation I am
> planning to do an MD simulation by reducing distance between end of the
> protein and edge of the box. Is this is physically significant? Then what
> is the optimum distance for that?
>

Your intent is to use periodic images of the peptide to study its aggregation? 
By allowing the peptide to see itself, you've violating the minimum image 
convention.  Such an approach is not sound.  If you want to study aggregation, 
put multiple peptides in the box like everyone else does :)

-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
http://mackerell.umaryland.edu/~jalemkul

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