Lecture2
Bölüm anahatları
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Molecular Dynamics simulation of pentane and calculation potential of mean force
Video 1: Here, we introduce pentane and visualize the molecule by using VMD. We have 2 different dihedral angles now. We investigate the configuration file.
For further information about configuration files:
https://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node26.html
Video 2: We calculate the potential of mean force (PMF) of pentane using its two dihedral angles, namely, C1-C2-C3-C4 and C2-C3-C4-C5. By using the inverse Boltzmann distribution, we compute the PMF. For the PMF calculations, we use:
PMF = -RTln(pif)where, R is the gas constant with units of kcal x K-1 x mol-1, and T is the temperature of the simulations; pif is the probability of dihedral angle. The value of R is given by the jupyter notebook as 1.985 x 10-3. Finally, by editing configuration file, we learn that we can manipulate the vdW between the two terminal atoms of a dihedral angle. Here, these are C1-C4 and C2-C5 atoms.
For further information about Boltzmann distribution, Wikipedia is informative:
https://en.wikipedia.org/wiki/Boltzmann_distribution
Video 3: After assessing vdW on/off pentane simulations, we discuss the changing energy landscape between the two simulations. To understand the reasoning, we retrieve the potential of the dihedral angle equation and visualize it using matplotlib. By observing the result, we understand the potentials (bonds, angles, dihedrals, and vdW interactions) that emerge as the PMF.
Video 4: The energy minimization process is investigated. The dihedral angle of butane is computed for the PMF, and an unfavorable conformation of butane is minimized. We run 1,000 steps of minimization using NAMD2. We then use the SciPy package to minimize the equation of the dihedral angle.Detailed information about minimization of NAMD2 and SciPy can be found at:
https://www.ks.uiuc.edu/Research/namd/2.14/ug/node36.html
https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.minimize.html
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