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From: Kateryna Miroshnychenko <kateryna_mirosh.ire.kharkov.ua>

Date: Thu, 14 Jul 2005 11:18:28 +0300

Dear All,

I wonder what is the meaning of 108.587 coefficient which is used to

convert eigenvalues of mass-weighted covariance matrix to sm^-1 (see

below part of the file analyze.c from ptraj). In what units are the

eigenvalues of mass-weighted covariance matrix before this conversion?

I suppose they are in A^2*amu?

Thanks,

Katya

______________________________________________

Convert eigenvalues to cm^-1

*/

for(i = 0; i < neval; i++){

if(eigval[i] > 0.0)

eigval[i] = 108.587 * sqrt(0.6/eigval[i]); /* "0.6" is conversion of kT for 300K into kcal/mol(?) */

else if (eigval[i] < 0.0)

eigval[i] = -108.587 * sqrt(-0.6/eigval[i]);

______________________________________________

********************************************

Kateryna Miroshnychenko

post-graduate student

Department of Biological Physics,

Institute of Radiophysics and Electronics,

National Academy of Sciences of Ukraine,

Kharkiv, Ukraine

E-mail:kateryna_mirosh.ire.kharkov.ua

********************************************

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Received on Thu Jul 14 2005 - 09:53:00 PDT

Date: Thu, 14 Jul 2005 11:18:28 +0300

Dear All,

I wonder what is the meaning of 108.587 coefficient which is used to

convert eigenvalues of mass-weighted covariance matrix to sm^-1 (see

below part of the file analyze.c from ptraj). In what units are the

eigenvalues of mass-weighted covariance matrix before this conversion?

I suppose they are in A^2*amu?

Thanks,

Katya

______________________________________________

Convert eigenvalues to cm^-1

*/

for(i = 0; i < neval; i++){

if(eigval[i] > 0.0)

eigval[i] = 108.587 * sqrt(0.6/eigval[i]); /* "0.6" is conversion of kT for 300K into kcal/mol(?) */

else if (eigval[i] < 0.0)

eigval[i] = -108.587 * sqrt(-0.6/eigval[i]);

______________________________________________

********************************************

Kateryna Miroshnychenko

post-graduate student

Department of Biological Physics,

Institute of Radiophysics and Electronics,

National Academy of Sciences of Ukraine,

Kharkiv, Ukraine

E-mail:kateryna_mirosh.ire.kharkov.ua

********************************************

-----------------------------------------------------------------------

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Thu Jul 14 2005 - 09:53:00 PDT

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