Research on Computational Chemistry and teaching activities developed in the group MoBioChem led by Dr. Juanjo Nogueira at the Faculty of Science of the Universidad Autónoma de Madrid.
Hi. There cannot be that total energy is constant, thus you cannot ignore this assumption, there is no point to ignore it in other words. What is constant is the energy of each macrostate. Thus, lnΩ or lnW should be lnW_i, where W_i is one of the macrostates. And n_k (I prefer n_j) should in reality be n_ik, where k = 0 to S-1, S is the number of energy levels. Sum(Ω_i) = Ω = (energy levels)^N
Thank you very much for the nice explanation!! I have one question: How do I get the P_u,i 's in the sum for the second equation (of the main ones that need to be solved self-consistently) to eventually get the whole P_u?
Is it me or does this actually relate to subject? Particle in a box model Thanks for your well produced video. Your viewers might enjoy seeing my personal amateur science project in the visual aid linked below. It uses a sheet of spring-like material buckled from the ends to form a Gaussian curve. This is to represents a two dimensional field with the ends bounded. Seeing the mechanical effect may also takes some of the mystery of what the math is showing. See the load verse deflection graph in the white paper found elsewhere on my RU-vid channel. ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-wrBsqiE0vG4.htmlsi=waT8lY2iX-wJdjO3
at 13.26, you wrote ensemble average in terms of q (stating integration over all coordinates except reaction coordinate). Later at 16.33, you have rewritten the ensemble average but in terms of reaction coordinates. How in first case, ensemble average was independent of reaction coordinate and in second it is not??? It is confusing. Plz clear it.
Dear Professor, I have a doubt. If we know the total bias potential, then it means that we know the unbias potential too. So doesn't knowing the unbias potential make known the path connecting the end states. Also, since we are using a force field, so we know the unbias potential beforehand, right?
Thank you, professor, for the great lectures. Can the LJ potential describe the interaction between more than two atoms, and if so, how will the profile change?
3:16 "and now with this biased potential we will run the MD simulation" but we don't know the unbiased potential beforehand. So how can we know the biased potential.
Indeed we compute the biased potential at each time step with the force field, so we know it. We don't know the overall potential energy landscape beforehand, but we know the potential at the current position, which is the only thing we need
@@thisiskurt the biased potential is the sum of the unbiased potential (the real one) plus the artificial potential. If you know the internal coordinates of the system (and we know it) we just replace the value of the coordinates in the potential function and we obtain the value of the potential, both the unbiased one and the artificial one
One has to create a library to define the atom nomenclature and atomic charger and to create a frcmod file to define the unknown force field parameters. It is not automatic. It requires a bit of human work
