Dear Daniel,
Thank you for the help.
-Chetna
On Fri, Feb 9, 2018 at 1:35 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> So quasiharmonic analysis (and the thermodynamic properties calculated
> from it) really only works well if your system has one very
> well-defined energy minimum (because of the underlying assumption of
> harmonic oscillation). Mike Gilson et al. published a very nice
> article a while back that goes into this in some detail:
> https://pubs.acs.org/doi/abs/10.1021/ct0500904
>
> Also, I've personally never found looking directly at the matrices to
> be very enlightening. You may want to also try the 'projection'
> command to projection your coordinates along the generated
> eigenvectors, along with the various types of 'modes' analysis you can
> do ('modes fluct' etc). See the cpptraj section of the Amber 17 manual
> for more details and examples.
>
> Hope this helps,
>
> -Dan
>
> On Tue, Feb 6, 2018 at 9:50 AM, Chetna Tyagi <cheta231.gmail.com> wrote:
> > Dear Amber users,
> >
> > I have performed simulations on a small peptide (18 residues). I
> performed
> > dihedral PCA on the results and analyzed correlation matrices to find out
> > correlated motions amongst various sections of the peptide. I read the
> > previous answers about the differences in PCA and quasi-harmonic
> analysis.
> >
> > Is it more beneficial to carry out quasi-harmonic analysis for such
> > motions? I don't really understand the idea behind it but I performed the
> > calculation. The matrix 'mwcvmat.dat' when plotted as a heatmap doesn't
> > show anything interesting in comparison to dihedral PCA matrices.
> >
> > Also the file 'thermo.dat' with thermo chemistry calculation and the
> first
> > 20 modes is produced. I am unable to apply the information to my
> simulation
> > results. Does it show stability in simulation? What does the various
> energy
> > terms calculated for each mode signify?
> >
> > I am attaching the heatmap of the matrix.
> >
> >
> > [image: Inline image 1]
> > Any help or advice is appreciated.
> > --
> > Best wishes
> > Chetna
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Best wishes
Chetna
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Received on Fri Feb 09 2018 - 07:30:04 PST
