Lecture1
Section outline
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Molecular Dynamics simulation of butane and analysis of torsion angle
Video 1: MD simulation of butane is performed, and visualization of butane in VMD is shown. PSF generation by using a topology file is also discussed. A quick look on force-field files gives an idea about potentials.
Video 2: Root mean squared deviation (RMSD) and the probability distribution of the torsion angle belonging to butane are analyzed by using a Jupyter-notebook. Favorable (more sampled) and unfavorable (less sampled) conformations are shown. Sampling and its effect on gathered information is discussed. If you want a detailed explanation of alkane conformations, take a look at Khan Academy’s lecture:
Video 3: Demonstration of the visualization of the torsion (dihedral) angle of butane using VMD, including the selection of atoms. Note that to visualize an atom, you may do it by pushing 1; for bonds, it is 2 (also you need 2 atoms for bonds); for angles it is 3 (and again you need 3 atoms for angles); finally, for dihedral (torsion) angles you should press 4, and you need 4 atoms to build a dihedral (torsion) angle.
Video 4: Topology file (top_all35_ethers.inp) and parameter file (par_all35_ethers.prm) are discussed. In the topology file, the bonds, angles, and dihedral angles of a molecule are stored as a library. By using topology file, we generate ‘psf’ file that is specific to our molecule, butane. To perform an MD simulation, potentials of these three factors and van der Waals (vdW) interactions are needed; hence we use the information in parameter file. Configuration file (extension of this file may be .namd or .conf) is needed to instruct NAMD2 software about the variables of simulation. Timestep is chosen as 1 fs, and 1,000,000 fs is 1 ns which is the length of our simulation. Nevertheless, we set the temperature here, which is 1,000 K.For further information about topology and parameter files:
https://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node24.html
https://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node25.html
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