SIMULATION IN CHEMISTRY & BIOCHEMISTRY

Chemistry 430

Spring Term 2017

Instructor: Jay Ponder


GENERAL INFORMATION

Syllabus & Schedule [PDF]


LECTURE SUMMARIES

Lecture 1 (Jan 18): Introduction to Molecular Modeling [PDF]

Lecture 2 (Jan 23): Introduction to Molecular Mechanics I [PDF]

Lecture 3 (Jan 25): Introduction to Molecular Mechanics II

Lecture 4 (Jan 30): Potential Energy Surfaces & Optimization Methods [PDF]

Lecture 5 (Feb 01): Basics of Molecular Dynamics Simulation I [PDF]

Lecture 6 (Feb 06): Basics of Molecular Dynamics Simulation II

Lecture 7 (Feb 08): Using Molecular Dynamics to Compute Properties [PDF]

Lecture 8 (Feb 13): Introduction to Monte Carlo Methods I [PDF]

Lecture 9 (Feb 15): Introduction to Monte Carlo Methods II

Lecture 10 (Feb 20): Methods for Free Energy Calculations [PDF]


READINGS & REFERENCES

Introduction to Using a Terminal Window (Unix/Linux)

Unix for the Beginning Mage, J. Topjian [PDF]

Useful Unix Tools [HTML]

Perspectives on Molecular Modeling

Biomolecular Modeling: Goals, Problems, Perspectives,
W. F. van Gunsteren, D. Bakowies, R. Baron, I. Chandrasekhar, M. Christen,
X. Daura, P. Gee, D. P. Geerke, A. Glattli, P. H. Hunenberger, M. A. Kastenholz,
C. Oostenbrink, M. Schenk, D. Trzesniak, N. F. A. van der Vegt and H. B. Yu,
Angewandte Chemie International Edition, 45, 4064-4092 (2006) [PDF]

Biomolecular Modeling and Simulation: A Field Coming of Age,
T. Schlick, R. Collepardo-Guevara, L. A. Halvorsen, S. Jung and X. Xiao,
Quarterly Reviews of Biophysics, 44, 191-228 (2011) [PDF]

Nonlinear Optimization Methods

Optimization Methods in Computational Chemistry, T. Schlick,
Reviews in Computational Chemistry, 3, 1-71 (1992) [PDF]

Molecular Dynamics Simulation

Molecular Dynamics, J. Meller,
Encyclopedia of Life Sciences, 1-8 (2001) [PDF]

Introduction to Molecular Dynamics Simulation, M. P. Allen,
Computational Soft Matter, NIC Series, 23, 1-28 (2004) [PDF]

Molecular Dynamics: Survey of Methods for Simulating
the Activity of Proteins, S. A. Adcock and J. A. McCammon,
Chemical Reviews, 106, 1589-1615 (2006) [PDF]

History of the Monte Carlo Method

Equation of State Calculations by Fast Computing Machines, N. Metropolis,
A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller and E. Teller,
Journal of Chemical Physics, 21, 1087-1092 (1953) [PDF]

Perspectives on "Equation of State Calculations by Fast Computing
Machines", W. L. Jorgensen, Theoretical Chemistry Accounts,
103, 225-227 (2000) [PDF]

The Beginning of the Monte Carlo Method,
N. Metropolis, Los Alamos Science, 14, 125-130 (1987) [PDF]

Scientific Uses of the MANIAC, H. L. Anderson,
Journal of Statistical Physics, 43, 731-748 (1986) [PDF]

Monte Carlo Theory and Algorithms

Progress and Outlook in Monte Carlo Simulations, D. N. Theodorou,
Industrial & Engineering Chemistry Research, 49, 3047-3058 (2010) [PDF]

Monte Carlo Simulations, D. J. Earl and M. W. Deem,
Methods in Molecular Biology, 443, 25-36 (2008) [PDF]

Monte Carlo Codes, Tools and Algorithms, D. Dubbledam, A. Torres-Knoop
and K. S. Walton, Molecular Simulation, 39, 1253-1292 (2013) [PDF]

Free Energy Calculations

Free Energy Calculations in Structure-Based Drug Design, M. R. Shirts,
D. L. Mobley and S. P. Brown, Chapter 5 from Drug Design: Structure- and
Ligand-Based Approaches, by K. M. Merz Jr., D. Ringe and C. H. Reynolds [PDF]

Towards Accurate Free Energy Calculations in Ligand
Protein-Binding Studies, T. Steinbrecher and A. Labahn,
Current Medicinal Chemistry, 17, 767-785 (2010) [PDF]

Efficient Estimation of Free Energy Differences from Monte Carlo Data,
C. H. Bennett, Journal of Computational Physics, 22, 245-268 (1976) [PDF]


SOFTWARE RESOURCES

Avogadro Molecular Editor

Avogadro 1.2.0 Software for MacOS [DMG]

Avogadro 1.2.0 Software for Windows [EXE]

Avogadro2 1.90.0 Software for MacOS [DMG]

Avogadro2 1.90.0 Software for Windows [EXE]

Learning Avogadro [PDF}

Avogadro Example Files [GZIPPED TAR}

Chimera: Extensible Molecular Modeling System

Chimera 1.11.2 Software for MacOS [DMG]

Chimera 1.11.2 Software for Windows [EXE]

Chimera Quick Reference [PDF]

Chimera Getting Started [HTTP]

Chimera User's Guide [HTTP]

VMD: Visual Molecular Dynamics

VMD 1.9.3 Software for MacOS [DMG]

VMD 1.9.3 Software for Windows [MSI]

VMD 1.9.3 User's Guide [PDF]

Using VMD Tutorial [PDF]

VMD Tutorial Files [GZIPPED TAR]

FFE: Force Field Explorer

Force Field Explorer 8.0 Software for MacOS [DMG}

Force Field Explorer 7.1 Software for Windows [ZIP}

Force Field Explorer Manual [PDF}

TINKER Software Tools for Molecular Design

TINKER 8.1 Software for MacOS [GZIPPED TAR]

TINKER Manual [PDF}

Spartan Molecular Modeling (Q-Chem)

Spartan Student Overview [PDF]

Spartan Student Tutorial [PDF]

Walking Through Spartan Student (input file for tutorial) [Input]

Spartan '14 Manual [PDF]

Q-Chem 4.1 Manual [PDF]

Gaussian Quantum Chemistry

Gaussian 09 Online Manual [HTML]

GaussView 5 Online Manual [HTML]

APBS Poisson-Boltzmann Solver

PDB2PQR Command Line Usage [HTML]

APBS Command Line Usage [HTML]

APBS Input Files & Options [HTML]

Tutorial: Lysozyme pKa Calculation [HTML]

Tutorial: Visualizing APBS Results in VMD [HTML]

SDA7 (Simulation of Diffusional Association, V7)

SDA7 Documentation [HTML]


LABORATORY PROJECTS

Suggested Lab Report Format [PDF]

Lab 1 (Jan 20): Unix Tutorial; Using Chimera, VMD, FFE & Spartan [Files]

Lab 2 (Jan 27): Conformational Analysis of Alanine Dipeptide [Files]

Lab 3 (Feb 03): Liquid Properties via Molecular Dynamics Simulation [Files]

Lab 4 (Feb 10): Global Optimization of Lennard-Jonesium & PolyAlanine [Files]

Lab 5 (Feb 17): Relative Hydration Free Energy of Monovalent Ions [Files]