Computational Chemistry (CHM579)

Description

This course provides a thorough grounding in the main techniques used in modern computational chemistry. The course contains a lab component where the students will learn practical aspects of using GROMACS and VMD packages. An undergraduate course in Physical Chemistry is a prerequisite.

Reading

Week 1. Intro to classical mechanics [pdf]; intro to statistical mechanics [pdf] [pdf]
Week 2. Monte Carlo simulations [pdf], [pdf]
Week 3. Molecular dynamics [pdf], [pdf]
Week 6. Force fields [pdf]

Labs

Lab 1. Introduction to Linux cluster. Monte Carlo algorithm.
MC program [zip]; lab manual [pdf].
Starter info about Linux [pdf]

Lab 2. Equation of state for Lennard-Jones fluid by Monte Carlo simulations.
Lab manual [pdf];
paper "The Lennard-Jones equation of state revisited", by J.K. Johnson, J.A. Zollweg and K.E. Gubbins, Molecular Physics, 1993, Vol. 78, 591-618 [pdf];
MC program mc-016-ru.f90, input file, and program for calculating averages [MC_program.zip].

Lab 3. MD simulation of water in GROMACS.
Lab manual [pdf];
paper "Diffusion constant of the TIP5P model of liquid water", by M.W. Mahoney and W.L. Jorgensen, J. Chem. Phys., 114, 361 (2001) [pdf];
input files for GROMACS simulations: [topol.top], [conf.gro], [grompp.mdp]; all files together [inputs.zip].

GROMACS workshop with lectures and tutorials

Lab 4. MD simulation of solvated acetone in GROMACS.
Lab manual [pdf];
paper "Kirkwood-Buff derived force field for mixtures of acetone and water", by S. Weerasinghe and P.E. Smith, J. Chem. Phys., 118, 10663 (2003) [pdf];
vizualization of GROMACS trajectories with VMD: [pdf];
input files for GROMACS simulations: [zip].

Lab 5. Molecular dynamics of lysozyme in water.
Lab manual [pdf]; files and scripts: [zip]

Lab 6. Simulation of water permeation through nanotubes.
Lab manual [pdf];

Lab 7. Polarizable force field.
Lab manual [pdf]; files: [zip];
EFP paper [pdf];
Water dipole moment paper [pdf];

Lab 8. Hydrated Ions.
Lab manual [pdf];
paper "Specific Ion Effects at the Air/Water Interface", by P. Jungwirth and D.J. Tobias, Chem. Rev. 106, 1259-1281 (2006) [pdf];
input files for GROMACS simulations: [zip].

Lab 9. Hydration free energy of ions.
Lab manual [pdf];
input files for GROMACS simulations: [zip].

Lectures and Notes

Quiz 12 answer keys[pdf]
2012 Midterm (open-book 2-hour exam) [pdf]
2012 Final (open-book 2-hour exam) [pdf]