Molecular Simulation

Physics 171.635: Spring 2007

Molecular Simulations: Methods and Applications

Page Contents:

Messages from the Professor

Homework 3 will be due on March 22 as indicated on the sheet.

Contact Information

Professor

Mark Robbins

mr at jhu.edu

410-516-7204

Bloomberg 317

Office Hours: TBA

Class:
9-10:30 AM Thursday and Friday in Bloomberg 178.

Course Description: This course will introduce students to the range of methods currently being used to simulate the behavior of matter at the molecular scale. The statistical mechanics underlying simulations will be briefly reviewed. Then basic methods for equilibrium Monte Carlo and molecular dynamics simulations will be described, including techniques for generating different ensembles and calculating free energies and phase equilibria. Methods for long-range potentials, biased Monte Carlo, accelerated dynamics, nonequilibrium systems and multiscale modeling will also be covered. Assignments will involve applying these methods to sample problems starting from existing sample code that may be useful in the student's future research.

Prereq: Simulations for a wide range of equilibrium and nonequilibrium applications, including hands-on experience with existing codes.

Prerequisite: Undergraduate course in statistical mechanics or permission from the instructor.

Textbooks:
Required: Understanding Molecular Simulation: From Algorithms to Applications, 2^nd edition by Daan Frenkel and Berend Smit.

Recommended: Computer Simulation of Liquids, M. P. Allen and D. J. Tildesley.

Grading:

The grading will be based entirely on homework.

Homework:
Solving problems is not only the best way to learn physics, it is the only way. For this reason, the problem sets are probably the most important part of the course. You may work together on the problem sets; however the final writeup should be your own. To get the greatest benefit from the problems sets you should attempt to think through every problem yourself before discussing it with others. Problem sets are due on the Friday the week after they were assigned. Late homework will be given reduced credit. No credit will be given for homework more than one week late without prior approval for a compelling reason.

Syllabus: Since this is a new course the syllabus will be updated as the course progresses. Introductory material will be adjusted to the preparation of the students enrolled in the course.

Week of	Subject Matter	Reading	Homework
Jan. 22	Statistical Mechanics and Monte Carlo	Chap. 2,3
Jan. 29	Monte Carlo and Molecular Dynamics	Chap. 3	Homework set 1
Feb. 5
Feb. 12	Molecular Dynamics	Chap. 4, App D	Homework set 2
Feb. 19	MD in different ensembles	Chap. 6
Feb. 26	Ensembles continued and fast force algorithms	App. A, B, E, F, handout	Homework set 3
Mar. 5	Long-range interactions	Chap. 12
Mar. 12	SPRING BREAK
Mar. 19	Monte Carlo in different ensembles	Chap. 5
Mar. 26	Free energy Calculations	Chap. 7	Homework set 4
Apr. 2	More on free energy, parallel tempering	Chap. 8, 10, 12
Apr. 9	Rare Events, Multiscale Methods	Chap. 16, review paper
Apr. 16	Multiscale methods + student presentations	Review papers	19^th –Yeh, Perilla 20^th – Paliwal, Echeverria
Apr. 23	Student presentations	Review papers	26^th – Nagarajan, Khangulov 27^th - Aksel, Yee, Erdemli

Homewood-wide statement on Disabilities

If you are a student with a disability or believe you might have a disability that requires accommodations, please contact Dr. Richard Sanders, Homewood Undergraduate Disability Services Coordinator, in the Office of Academic Advising, Garland Suite 3A, (410) 516-8216, sanders@jhu.edu , to discuss reasonable and appropriate accommodations.

University-wide statement on Academic Ethics

The strength of the university depends on academic and personal integrity. In this course, you must be honest and truthful. Ethical violations include cheating on exams, plagiarism, reuse of assignments, improper use of the Internet and electronic devices, unauthorized collaboration, alteration of graded assignments, forgery and falsification, lying, facilitating academic dishonesty, and unfair competition. As noted above, collaboration on homework sets is encouraged. However, you should attempt problems independently before collaborating and must write up your homework independently.

Report any violations you witness to the instructor. You may consult the associate dean of students and/or the chairman of the Ethics Board beforehand. See the guide on "Academic Ethics for Undergraduates" and the Ethics Board web site (http://ethics.jhu.edu/ ) or http://www.advising.jhu.edu/ethics.html for more information.