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Molecular Modeling and Computer History

This document summarizes the topics and methods covered in a molecular modeling course, including forces between molecules, molecular mechanics, Monte Carlo and molecular dynamics simulations, and quantum modeling methods like Hartree-Fock and density functional theory. It notes there will be hands-on computational assignments and a final project. Students will use modeling to perform experiments, construct theories, and compare results to test models and theories.

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Caroline
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13 views5 pages

Molecular Modeling and Computer History

This document summarizes the topics and methods covered in a molecular modeling course, including forces between molecules, molecular mechanics, Monte Carlo and molecular dynamics simulations, and quantum modeling methods like Hartree-Fock and density functional theory. It notes there will be hands-on computational assignments and a final project. Students will use modeling to perform experiments, construct theories, and compare results to test models and theories.

Uploaded by

Caroline
Copyright
© All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd

2/2/16

CBE 422
Molecular Modeling Methods
n  Forces between molecules
n  Molecular mechanics
n  Classical molecular simulation methods:
Monte Carlo + Molecular Dynamics
n  Quantum modeling: Hartree-Fock and density
functional theory methods

n  Hands-on, computational assignments


n  Final project on mutually agreed-upon topic

Time and Length Scales

source: [Link]

1
2/2/16

Early History of Computers

n  John von Neumann (1903-1957),


among first four faculty of IAS:
Princeton “stored program+data”
versus Harvard architecture
n  ENIAC (1946) – U. Penn
n  UNIVAC (1951) – U.S. Census J. Robert Oppenheimer and John von
Bureau Neumann in front of the Institute computer
(IAS Archives photo)
n  IBM 650 (1954) – 1st mass-produced
n  DEC PDP 8 (1965) – 1st minicomputer
n  CRAY I (1976) – vector
“supercomputer”
n  Today: “commodity” clusters

[Link]/timeline/
[Link]/wiki/Harvard_architecture
[Link]/wiki/John_von_Neumann
This NY Times article
ENIAC - U. S. Army Photo

[Link]

2
2/2/16

[Link]

http://
[Link]/
researchcomputing/
computational-
hardware/

3
2/2/16

Real Make Model


Systems models Systems

Perform Perform Construct


experiments simulations theories

Experimental Simulation Theoretical


data results predictions

Compare to test Compare to test


models, theories
understand
physics, make
predictions

Adapted from Allen and Tildesley, Computer Simulation of Liquids, Oxford 1987

Computer Software
n  Operating System (Mac OS, Windows,
Unix/Linux)
n  Applications (e.g. Matlab, Hyperchem)
n  Open-source packages (e.g. Towhee,
LAMMPS, Gromacs)
n  User Code
¨ Compiled programs (Fortran or C)
¨ High-level scripting (e.g. Python)

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2/2/16

The first “bug”


Moth found trapped between
points at Relay # 70, Panel
F, of the Mark II Aiken Relay
Calculator while it was being
tested at Harvard University,
9 September 1945.
Lieutenant Grace Murray
Hopper affixed the moth to
the computer log, with the
entry: "First actual case of
bug being found". She put
out the word that she had
"debugged" the machine,
thus introducing the term
"debugging a computer
program”.

[Link]

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