[gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

Justin Lemkul jalemkul at vt.edu
Mon Sep 21 14:18:25 CEST 2015

On 9/21/15 4:00 AM, Naba wrote:
> Dear Gromacs users and Developers,
> I have performed dihedral PCA for 4 extracellular loops of a transmembrane
> protein after successfully finishing 100 ns of simulation at 300 and 310 K.
> I obtained figures for each loops for two different temperatures as in this
> link: http://s28.postimg.org/dlva5i42l/d_PCA.jpg .
> As we can see in that figure that, the loop L1 has got only one minimum at
> both temperatures, whereas, L2 and L3 have got 4 minima at 300 K. I have
> also calculated the amount of frames in percentages at their respective
> minima. It seems that L2 and L3 have got more number of frames at their
> minima when combined in comparison to L1. Now my question is:
> Can we say that L2 and L3 are tend to be more stable at 300K than that of
> L1 at the both temperatures?

I wouldn't make any argument about "stability" here.  Conformational sampling, 
maybe, but the question is whether or not these PCs are the same between the 
different simulations.  If you're not projecting one trajectory onto the other's 
eigenvectors, you're quite possibly comparing apples and oranges.



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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