[gmx-users] CNT ROTATION

[Justin Lemkul]

On 5/29/14, 3:41 PM, ANDRES ADOLFO ORTEGA GUERRERO wrote:
> Should i try instead different pull MD(changing the pbcatom, CNT's COM,
> velocity,force) , in order to get new configuration for an umbrella
> sampling simulation and a PMF in z Axis calculation, until i´ll get no
> rotation in the CNT?

There may be other options, sure, but realize that no one on the list has 
sufficient information based on your description or stated goals to really tell.

> or can i used this MD, to get the configuration for the Umbrella Sampling??
>

It sounds like your observed behavior is non-physical and does not necessarily 
address what you're trying to study.  Based on the information at hand, I'd say no.

-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 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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