[gmx-users] hydrogen bond analysis

[Justin Lemkul]

On 10/29/13 5:46 PM, larif sofiene wrote:
> Greeting
> I'm working on a MD of a ligand-protein complex during 40 ns
> i want to analyses ligand-protein interaction hydrogen bonds
>
> My first question :
> Should i analyses a minimized frame from clustering of the trajectory
>             or should i analyses hydrogen bond occupancy over trajectory ?
>

I would think that a time average is much more useful than any single frame.

> My second question :
> Is it more correct if i do my analysis over the equilibrated phase of MD
> (based on RMSD, radius of gyration , etc ...) for example the last 10 ns,
> than doing it over the whole trajectory (40 ns) ?.
>

Allowing for equilibration time is generally a good idea.

-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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