Re: [AMBER] RMSD for two trajectories

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Wed, 22 Dec 2010 18:39:45 -0800

> I have two trajectories of MD simulation related to wild type and mutant
> form of my ligand in the complex of receptor-ligand. I would like to compare
> the RMSD of pairwise structures but I have not found any option in VMD in
> order to do that. How can I compare the RMSD of two seperate trajectories.

My remarks assumed that for trajectories T1 and T2, you'd be doing
rms of frame T1.1 to T2.1, T1.2 to T2.2, and so on. On second
reading, I'm not so sure that's what you meant. Per Setyanto's
suggestion, you might also want to compare RMSD of each trajectory
with respect to its starting structure by simply graphing the two
plots together. This is completely doable with ptraj and a graphing
program like gnuplot. Another possibility would be to cluster each
trajectory, obtaining an average structure for each cluster, and
compare those structures. Again, other software would be required to
compare chemically different structures, but the advantage would be
that the comparison would be more meaningful than would be the case
for my original assumption.


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Received on Wed Dec 22 2010 - 19:00:03 PST
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