[gmx-users] How much different run (with posre.itp) from no posre.itp?

[Justin Lemkul]

On 11/11/14 12:30 AM, Batdorj Batsaikhan wrote:
> Dear gmx-users,
>
> I run 3 different conformation of a protein. I run 2 of them no posre.itp and another one has posre.itp. How much different these two run?
>

Impossible to tell.  You've got too many variables - different conformations, 
different application of restraints, as well as (presumably) different random 
velocities at the outset of each run.  Even if you could control for different 
factors, I don't know what you'd hope to learn by comparing such 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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