[gmx-users] On the box type

[Justin Lemkul]

On 7/7/13 11:00 AM, akcyrus wrote:
> Dear all,
> The only tutorial on umbrella sampling by Justin (
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html)
> assumes a rectangular box and pulling is done to separate chains. Is it
> true that the approach worked solely because one of the reference chains
> was position restrained as that did not allow it to rotate.

Yes, the restraints prevent rotation while simultaneously serving other purposes 
(explained in the tutorial and associated paper).  Please note that I also did 
analysis to determine that no spurious interactions occurred across PBC for this 
system.  Normally, one would not use a rectangular box for a non-restrained 
system, though you should not necessarily view restraints as some generalized 
"solution" for the rotation problem - the general solution is to use a box that 
reflects the rotational symmetry of the system.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Associate

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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