[gmx-users] simulated annealing

[Justin Lemkul]

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On 11/16/13 8:14 PM, Raghunath Satpathy wrote:
>
>
> is it necessary to heat and cool protein in simulated annealing ? i wanna to check thermostability by md simulation only by increasing temp (without cooling ) in many picoseconds , is it possible to get good result ? pls reply soon
>

What is "necessary" depends on what you are trying to achieve.  See what others 
do in the literature and develop a protocol based on what seems sensible.  For 
thermostability assessments, I don't see any immediate need to cycle 
temperatures up and down.  Simple heating could be perfectly reasonable.

-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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