[gmx-users] Structures after Dihedral principle component analysis (dPCA)

soumadwip ghosh soumadwipghosh at gmail.com
Thu Dec 28 23:37:18 CET 2017


Please ignore my previous incomplete mail.

It seems that you have got PC1, PC2 and Gibb's free energy in the x, y and
z axes respectively. If I am not wrong you first combined the pc1.xvg and
pc2.xvg to a single .xvg file compatible with gmx sham. Right? Then, You
must have converted the .xpm output from gmx sham to a text file and
plotted using matlab/mathematica. In any of the above if you click on the
valley corresponding to the free energy minima it should show you the
coordinate of that point. Now, from this you know what is the PC1 and PC2
of your FEL. Now go back to your combined .xvg file to find out what is the
corresponding time stamp of that. Once you get this, it should not be a
problem dumping out that particular snapshot using gmx trjconv.

Soumadwip Ghosh

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