Molecular Dynamics Simulations of Small Molecules
Konu özeti

Molecular Dynamics Simulations of Small Molecules
Skill Level: Intermediate
Language: English
Workload: 2 hours total
Topic: Computational chemistry
Overview:
Lecture 1 – Molecular Dynamics simulation of butane and analysis of torsion angle
Lecture 2 – Molecular Dynamics simulation of pentane and calculation potential of mean force
Lecture 3 – Molecular Dynamics simulations of multiple ethane molecules in water box and calculation of diffusion coefficient
Course Description: Molecular dynamics (MD) simulations of small molecules, such as ethane, butane, and pentane, are performed in an applied manner. The MD simulations are executed using NAMD, and the visualization of the simulations is done with VMD. The analyses of features and material properties of molecules are calculated using the Python programming language.
Course Contents:
Lecture 1 – Molecular Dynamics simulation of butane and analysis of torsion angle
Lecture 2 – Molecular Dynamics simulation of pentane and calculation potential of mean force
Lecture 3 – Molecular Dynamics simulations of multiple ethane molecules in water box and calculation of diffusion coefficient
Who Should Enroll: Anyone who wishes to learn running and analyzing an MD simulation.
Prerequisite(s):
Basics of Molecular Dynamics simulation and its analyses
An indepth information of forcefields
Computing energy surface of a small molecule
Bonded and nonbonded interactions that govern dynamics
Tools, libraries, frameworks used: Python, VAMD, NAMD2
Learning Objectives:
Basics of Molecular Dynamics simulation and its analyses
An indepth information of forcefields
Computing energy surface of a small molecule
Bonded and nonbonded interactions that govern dynamics
About the instructor(s): https://midst.sabanciuniv.edu/people.html

Course Overview
 To download NAMD2 and VMD please visit:
https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD
https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
 The recommended versions for NAMD2 and VMD are 2.14 and 1.9.4. However, feel free to experiment on NAMD 3.0, since it has new features (like using GPU more efficiently).
 For adding NAMD2 and VMD as path variables please see: HowTo_VMD_NAMD.pdf
 Please find pythonica.pdf for instructions of python installation.
 To download NAMD2 and VMD please visit:

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 forcefield 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 Jupyternotebook. 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/namdtutorialunixhtml/node24.html
https://www.ks.uiuc.edu/Training/Tutorials/namd/namdtutorialunixhtml/node25.html

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/namdtutorialunixhtml/node26.html
Video 2: We calculate the potential of mean force (PMF) of pentane using its two dihedral angles, namely, C1C2C3C4 and C2C3C4C5. 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 K1 x mol1, 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 103. 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 C1C4 and C2C5 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

Molecular Dynamics simulations of multiple ethane molecules in water box and calculation of diffusion coefficient
Video 1: Solvation of 10 ethane molecules using a water box is shown. The process is done by using the GUI of VMD and a homemade TCL code. A glimpse of ionization (adding salt) is also demonstrated.
Video 2: After scrutinizing the configuration file, the MD simulation of ethane molecules is visualized in VMD. Periodic boundary conditions (PBC) and Langevin temperature/pressure control are briefly mentioned.
Wikipedia pages for PBC and Langevin dynamics are informative:
https://en.wikipedia.org/wiki/Periodic_boundary_conditions
https://en.wikipedia.org/wiki/Langevin_dynamics
Video 3: The diffusion coefficient and heat capacity are computed using a Jupyter notebook. Mean squared deviation (MSD) is used for the calculation of the diffusion coefficient.For the relation of slope and diffusion please see:
https://mathbench.umd.edu/modules/cellprocesses_diffusion/page10.htm
A good random walk guide:
https://en.wikipedia.org/wiki/Random_walk
Nevertheless, for heat capacity:
https://en.wikipedia.org/wiki/Heat_capacity
Video 4: Advanced visualization in VMD is demonstrated using the MD of ethane molecules.