[gmx-users] entropy from eigenfrequency

[nahren manuel]

Dear Gromacs Users,

I was just wondering if the formula and the units which I use for getting the entropy is absolutely correct. 

The eigenfrequency (v) in cm-1 are obtained from eigenfreq.xvg.( GMX ver 4.0.7, using normal mode calculations)

TS = [alpha/exp(alpha)-1] -  log[1-exp(-alpha)]
where alpha = (h*v)/kbT, 

h=Planck's const. ; kb= Boltzmann Constant; T=temperature.

Does the unit conversion result TS is kJ/mol (I feel yes, but I want to be sure)?
My values are,
T(D)S = 415305.23 (complex) - 315149.18 (protein1)  -  100122.14 (protein2) 
So, T(D)S = 33.91 kJ/mol

Best,
nahren

My above conclusions are based on  Gromacs source code,
/* Gromacs units are kJ/(mol*nm*nm*amu),
   * where amu is the atomic mass unit.
   *
   * For the eigenfrequencies we want to convert this to spectroscopic absorption
   * wavenumbers given in cm^(-1), which is the frequency divided by the speed of
   * light. Do this by first converting to omega^2 (units 1/s), take the square 
   * root, and finally divide by the speed of light (nm/ps in gromacs).   
   */
  factor_gmx_to_omega2       = 1.0E21/(AVOGADRO*AMU);
  factor_omega_to_wavenumber = 1.0E-5/(2.0*M_PI*SPEED_OF_LIGHT);  
    
  for (i=0; i<=(end-begin); i++)
  {
      value = eigenvalues[i];
      if(value < 0)
          value = 0;
      value=sqrt(value*factor_gmx_to_omega2)*factor_omega_to_wavenumber;
      fprintf (out,"%6d %15g\n",begin+i,value);
  }
  fclose(out);
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