<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear Gromacs Users,<br><br>I was just wondering if the formula and the units which I use for getting the entropy is absolutely correct. <br><br>The eigenfrequency (v) in cm-1 are obtained from eigenfreq.xvg.( GMX ver 4.0.7, using normal mode calculations)<br><br>TS = [alpha/exp(alpha)-1] - log[1-exp(-alpha)]<br>where alpha = (h*v)/kbT, <br><br>h=Planck's const. ; kb= Boltzmann Constant; T=temperature.<br><br>Does the unit conversion result TS is kJ/mol (I feel yes, but I want to be sure)?<br>My values are,<br>T(D)S = 415305.23 (complex) - 315149.18 (protein1) - 100122.14 (protein2) <br>So, T(D)S = 33.91 kJ/mol<br><br>Best,<br>nahren<br><br>My above conclusions are based on Gromacs source code,<br><span style="font-family: monospace;">/* Gromacs units are kJ/(mol*nm*nm*amu),<br> * where amu is the atomic mass
unit.<br> *<br> * For the eigenfrequencies we want to convert this to spectroscopic absorption<br> * wavenumbers given in cm^(-1), which is the frequency divided by the speed of<br> * light. Do this by first converting to omega^2 (units 1/s), take the square <br> * root, and finally divide by the speed of light (nm/ps in gromacs). <br> */<br> factor_gmx_to_omega2 = 1.0E21/(AVOGADRO*AMU);<br> factor_omega_to_wavenumber = 1.0E-5/(2.0*M_PI*SPEED_OF_LIGHT); <br> <br> for (i=0; i<=(end-begin); i++)<br> {<br> value = eigenvalues[i];<br> if(value < 0)<br> value = 0;<br>
value=sqrt(value*factor_gmx_to_omega2)*factor_omega_to_wavenumber;<br> fprintf (out,"%6d %15g\n",begin+i,value);<br> }<br> fclose(out);</span><br></td></tr></table>