Re: AMBER: ptraj analyze matrix entropy

From: Marcin Krol <>
Date: Thu, 6 May 2004 15:48:02 +0200 (METDST)

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

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
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

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.

marcin krol
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Thu May 06 2004 - 14:53:00 PDT
Custom Search