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

Naba nabajyoti.goswami at gmail.com
Sat Sep 26 07:19:46 CEST 2015

Dear David sir,

Is it feasible to evaluate Gibbs free energy landscape of only the
concerned loops from cartesian coordinates?
I mean to say is it feasible to extract covariance matrix of my concerned
loops from the entire trajectory and then evaluating Gibbs free energy
OR, should I extract trajectories of each and every loops separately and
calculating extract covariance matrix of each loop and then should I see
the Gibbs free energy landscape?

On Thu, Sep 24, 2015 at 7:42 PM, David van der Spoel <spoel at xray.bmc.uu.se>

> 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
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Nabajyoti Goswami

Research Associate
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India

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