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From: Marcin Krol <mykrol.cyf-kr.edu.pl>

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

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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Received on Thu May 06 2004 - 14:53:00 PDT

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

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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Received on Thu May 06 2004 - 14:53:00 PDT

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