[gmx-users] Dihedral energy map along two eigenvectors to actual conformations

[Ali Naqvi]

>
> Yes I have been using the how-to for making the energy landscape. Now I
> just need to go backwards.
>
> Ali Naqvi wrote:
> > Hi all,
> > I have been following the method outlined by Yuguang Mu to generate the
> > energy landscape along two eigenvectors. There are four minima that I
> > wish to explore. I can determine the points along the vectors that
> > correspond to the conformation, but am unsure of how to use those to
> > obtain the corresponding pdb as was shown in the paper:
> >
> > Mu, et al. Energy Landscape of a Small Peptide Revealed by
> > Dihedral Angle Principal Component Analysis, 2005.
> >
> > Any insight?
> >
>
> Have you tried the dihedral PCA how-to?  I don't know if it will give you
> everything you want, but it's certainly a start.
>
> http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA
>
> -Justin
>
> > Cordially,
> > Ali
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
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> End of gmx-users Digest, Vol 78, Issue 212
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