[gmx-users] A small Questions of umbrella samping

Justin Lemkul jalemkul at vt.edu
Sat Dec 6 15:07:47 CET 2014

On 12/6/14 3:59 AM, vg wrote:
> Dear Justin
> thank you for your reply.
> i have thought about the possibility you said before, but some paper make me confuse.
> the paper at: dx.doi.org/10.1021/ja303286e | J. Am. Chem. Soc. 2012, 134, 10959−10965 and PLOS Computational Biology | www.ploscompbiol.org 3 January 2014 | Volume 10 | Issue 1 | e1003417.
> they use CGMD simulation to calculate PMF of two big protein in the membrane, the PMF image which they get also have a steep increase
> at small values along the reaction coordinate. so, why?
> i put these figures at:
> https://t.williamgates.net/thumb-4EA4_5482C129.jpg
> https://t.williamgates.net/thumb-FA03_5482C129.jpg
> https://t.williamgates.net/thumb-E3CB_5482C129.jpg
> https://t.williamgates.net/thumb-F117_5482C4F9.jpg

Most of those images are too small to have their axes legible, but you need to 
realize that different systems have different geometries and the reaction 
coordinates appear (maybe? again, illegible in a couple cases) to be over 
different length scales.  You're comparing apples and oranges; trying to make 
one outcome look like another is unproductive.



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


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