Dear All
I am trying to find the configurational entropy for my DNA molecule in different elongations. However, to keep the molecule in each extended elongation in the production run, I applied harmonic constraint so that it won't relax towards equilibrium.
To calculate the configurational entropy, I used quasi-harmonic analysis. However, the entropy for all the elongations showed pretty much the same number, only differing in the digits after decimal. WHY is that so? clearly the corresponding entropy at the length 45A0 should be different from the one corresponding to the length 85 A0.
My guess is that it is calculating the entropy of the constraining force, because in all the production runs corresponding to different lengths, I have employed the same input files with the restraining constant k=100 to keep the molecule in that particular extension.
My second question is why do I see translational, vibrational, rotational entropy contributions listed in the thermo.dat file along with the total entropy while I have already did rms to the first frame, find the average, and then rms to the average structure to REMOVE THE GLOBAL TRANSLATIONS AND ROTATIONS. I was expecting only vibrational entropy???
My third question is when we are trying to find the entropy, the number of eigenvectors in front of "vecs" in the diagmatrix command should be the same as the number of atoms in the mask whose average structure was computed a few steps earlier. Is that right? Because my intuition says to find the entropy, we should take into account all the degrees of freedom except hydrogen atoms for example in a DNA molecule, or only backbone atoms in protein systems?
My last question is after doing quasi-harmonic analysis yielding the evecs.dat file containing the eigenvectors of the atoms in the mask , the evecs.dat file is in fact containing the matrix multiplication of the mass matrix and the fluctuation matrices. Is that right?
I would appreciate any insight into this.
Regards
Ramin
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Received on Tue Jul 18 2017 - 22:00:02 PDT
