[gmx-users] Fwd: plotting the displacement of each C-alpha along first eigenvector having largest eigenvalue

[Tsjerk Wassenaar]

---------- Forwarded message ----------
From: sunita gupta <sunita.bio at gmail.com>
Date: Fri, Aug 1, 2008 at 1:12 PM
Subject: plotting the displacement of each C-alpha along first
eigenvector having largest eigenvalue
To: tsjerkw at gmail.com


Hello

I have done 15 ns MD to study the effect of point mutation, comparing
it with wild one for this I want to calculate the displacement caused
by all alpha carbons from their initial position till last step...In
one of the article entitled "Effect on DNA relaxation of the single
Thr718Ala mutation in human topoisomerase I: a functional and
molecular dynamics study" they have calculated the displacement caused
of alpha carbon along eigenvector using largest eigenvalue..and on the
basis it is concluded which regions are displacing more....I have done
covariance analysis using g_covar.....but do not know how to go for
displacement calculation.....

Waiting for your kind reply
Thanks

--
SUNITA GUPTA
Member Research Team
Lead Invent Technology
TBIU, IIT Delhi, India
Email- sunita at leadinvent.com
Ph- +9111 26581524 (Ex-6)



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623