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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