AMBER: units of mwcovar matrix befor conversion

From: Kateryna Miroshnychenko <>
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?


  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

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