[gmx-users] Regarding gmx-user mailing list thread "Gibbs free energy landscape Vs. the stability of protein structure"

[David van der Spoel]

On 24/09/15 13:54, Nabajyoti Goswami wrote:
> Sir,
> I am a very big fan of yours and I deeply apologize for mailing this way.
> Actually I need some outcome within a very short period of time. So, I
> could not wait for the mailing lists answers.
>
> Coming to the point.. Can you please explain the tricks of dihedral PCA?
> You answered as my sampling was far from being complete because of the
> huge differences between my chosen temperatures 300K and 310K, then how
> can I make some comments at least, if my results are inconclusive. So
> far as stability point of view, how do I set my MDs?
As I said you may be sampling different part of phase space, but it 
could also be that it is something very similar in cartesian space.
The simple recommendation is do not use dihedral PCA at all but 
something in cartesian space.
>
> I have attached another figure (3D version of the previously generated
> figure). But I am a bit in confusion to analyze them.
>
> Please help a little sir.
>
> Regards,
>
> Yours truly
>
>
> Nabajyoti Goswami
>
> Bioinformatics Infrastructure Facility
> Department of Animal Biotechnology
> College of Veterinary Science
> Assam Agricultural University
> Khanapara, Guwahati 781022
> Assam, India


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se