On Mon, Oct 08, 2007, Marius Retegan wrote:
> I'm trying to use ptraj to calculate the entropy for o small ligand
> from a dcd trajectory.
> I've used the following input
> ================================
> trajin inhibitor.dcd
> rms first *
> matrix mwcovar name mwcvmat
> analyze matrix mwcvmat thermo reduce
> go
> ================================
> If I align the structures using rms first * I get high energy for the
> last 6 frequencies
This is correct (i.e. what you should expect). In principal component
analysis, there is no net rotational or translational motion (since you
aligned the frames), and this appears as a very large force constant for
these modes.
...hope this helps....dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | skype: dacase
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Wed Oct 10 2007 - 06:07:21 PDT
