[gmx-users] Umbrella Sampling

[Justin Lemkul]

On 1/31/14, 10:18 AM, Guo, Yanan wrote:
> Hello Dear Justin,
>
> In your Umbrella Sampling tutorial, why did you perform a brief NPT equillibration in each window before starting umbrella sampling?
>
> Is this brief equilibration necessary for all users or only for this tutorial?
>

Every umbrella sampling window is a new simulation, and the tutorial chooses a 
method whereby a nonequilibrium condition (SMD) is applied to generate the 
starting configurations.  You're going to have to throw out some amount of data 
anyway for equilibration, but a restrained equilibration beforehand can help 
speed things up and reduce the likelihood of instability.

-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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