AMBER Archive (2005)

Subject: AMBER: units of mwcovar matrix befor conversion

From: Kateryna Miroshnychenko (kateryna_mirosh_at_ire.kharkov.ua)
Date: Thu Jul 14 2005 - 03:18:28 CDT

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_at_ire.kharkov.ua
********************************************

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