[gmx-users] Identifying representative structures from a g_sham generated 2d energy plot

[bipin singh]

Hello,
Since you already built 2-d free energy landscape (FEL), you should
have PCs (PC1 and PC2) as a function of time. You also know from the
minima of FEL at which PCs the system spends longer time. Once you
find those PCs you should find when the system has those PCs (from PC
vs time). Then you should visualize your trajectory and check the
structures at those periods of time. Once you collect all the
structures you can pick the representative structure.
On Fri, Sep 16, 2011 at 15:21, Bailey A. <ab604 at soton.ac.uk> wrote:
> Hi,
>
>
>
> Having used g_sham to plot  a Gibbs free energy landscape using a projection
> of the first two principal components from the normal covariance analysis
> (not dihedral PCA) like so:
>
>
>
> g_sham -f 2dproj_1_2.xvg -ls gibbs.xpm -notime
>
>
>
> I would like to now identify which parts of the trajectory are represented
> by the various parts of the landscape. Are there simple steps to work
> through to do this?
>
>
>
> Having looked through the manual, previous user-list correspondence and
> output files I can see the bins and their contents and cross reference that
> with the log and ener.xvg, but I got a bit stuck after that.
>
>
>
> I also had a read of the David Leitner paper from 2007 where they identify
> structures from dPCA generate plot, “By quenching the structures in the
> space of the first two dPCA eigenvectors”, but I wasn’t really sure what
> this means.
>
>
>
> Any clues to get me started would be much appreciated.
>
>
>
> Alistair
>
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-- 
-----------------------
Regards,
Bipin Singh
IIIT-Hyderabad
INDIA