[gmx-users] initial position?

[Justin Lemkul]

Please keep the discussion on the mailing list.

On 3/10/15 2:54 PM, Sadeghi, Ehsan wrote:
> Thanks Justin. Do you mean that If I run using different positioning of
> molecules I will expect different results? How should I do sampling? Should I
> run for couple of times and do some sort of averaging?
>

With proper sampling, things should converge to the same outcome (on average). 
When you placed your molecules with some orientation(s) and positions, you're 
assuming that the configuration is in some way meaningful.  But in most cases, 
you have no real clue if that's true.  So multiple configurations, especially in 
cases like these, are particularly important.  You then analyze any physical 
observable of interest to see what the behavior is during each simulation and 
across simulations.

-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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