On Thu, Jan 05, 2012, Mahendra B Thapa wrote:
> I got the output files after 50 nS molecular dynamics
> simulation of a protein using AMBER 11. Let me help how to process these
> data to get spectral density to get plot of J(0) and residue number.
You need to state which "spectral density" you are interested in. Generally,
Amber supports calcualtion of time-correlation functions (see the ptraj
section of the manual). J(0) is just the area under the C(t) curve, but you
would have to calculate that yourself (either by numerical intergration, or by
fitting C(t) to some analytic function, the integrating the latter.)
...good luck....dac
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Received on Sat Jan 07 2012 - 10:00:04 PST
