Dear amber users,
I am using ptraj to determine the diffusion rate and correlation time of a
trisaccharide, from two 10-ns MD simulations. The only difference between
the simulations, is the retention of translational and rotational COM
motions in one (nscm=0).
The graphs I get from the ptraj correlation analysis, do not decay smoothly.
I have attached the graphs I get from the ptraj analysis.
Here is my input:
1. Correlation:
trajin md.crd
correlation cor2 :3.C1 :3.H1 1 20000 20000 out res3C1_res3H1_corr.out go
Any help will be greatly appreciated. I would also like to know what the
three columns stand for.
Thanks,
austin-
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Nov 22 2006 - 06:07:46 PST
