AMBER Archive (2004)

Subject: Re: AMBER: ptraj analyze matrix entropy

From: Marcin Krol (mykrol_at_cyf-kr.edu.pl)
Date: Thu May 06 2004 - 08:48:02 CDT

Thank you for your answer.
I have tried to calculate mass weighted covariance matrix and analyze it,
obtaining entropy contributions. the ptraj script that does it is very
simple:

trajin traje.file (I have oriented all frames on the starting structure)
matrix mwcowar name mwc200 out mwc200.dat start 1 stop 201
analyze matrix mwc200 out mwc200_ana.dat thermo vecs 0

However, if the number 3*N (N-atoms) is larger than 200 I get starnge
results:
1. I get a warning: setting vibrational entropy to zero for mode 201 with
vtemp = -319766250.735258
List of these warnings is continued til the last mode
2. I get a warning: assumption of classical behaviour for rotation
           may cause significant error
        (this is presumably due to high principal moments of inertia
(nuclei only) in amu-A**2:
3. I don't get zero point vibrational energy
4. Starting from node 201 I get unreasonalby huge E and vibrational
frequencies.

I know I can just ignore higher modes as they contribute very little to
the total entrophy, but in case of a large protein 200 first nodes not
necessarily include all the entropy.

When I look into the output file of the analyze matrix command I notice
that starting from node 201 I get huge negative frequencies. No matter how
many atoms I include in my calculations, I always get strange results if
the number of modes is higher than 200. When number of nodes < 200
everything seems to be fine. What is the reason for this??

I wonder also if the values given at the beginning of the analyze matrix
output file are eigenvalues?

Thank you in advamce for your answers.

Sincerely
marcin krol
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