Computational Science & Modeling and WebMO

IntroductionChemistry I Spring 2010

– Understand what CSM is

– Be able to apply WebMO in learning chemistry

Goals

• Computational Science & Modeling• Use of computers to help gain scientific

understanding (Brent Krueger, Hope College)• Example• Weather forecasting

What is CSM?

http://weather.unisys.com/

• CSM is key component of scientific discovery– Formerly: theory and experiment– Now: theory, experiment, and CSM (Three Pillars)

• Allows both very difficult problems and simple problems on very large/complex systems

• Essential in nearly all disciplines – Used by faculty in every science dept. at Hope

(chem, bio, physics, engineering, computer science, math, nursing, psychology)

• Students interested in science must have basic understanding of what CSM is.

Who cares about CSM?

• Most Chem CSM is either classical mechanics or quantum mechanics– Classical mechanics is simpler model (ignores

electrons) – used to study motions in very large systems (Molecular Dynamics)

–Quantum mechanics involves a full treatment of all electrons in system using Schrödinger Equation.• Apply using sophisticated computer programs

(Gaussian, MOPAC, GAMESS, NWChem, HyperChem, etc.)

• These programs are notoriously difficult to use and often expensive (though some are free)

CSM in Chemistry

Hardware, Software, Experience◦ Hardware provided by the Midwest Undergraduate

Computational Chemistry Consortium (MU3C)◦ Software (e.g. Gaussian) provided by MU3C◦ Experience will come as you practice using

WebMO

How can you use CSM?

Where else is CSM applied in everyday life?

Your Turn

Traffic flow modeling Genome sequencing (e.g. Human Genome

Project) Fluid dynamics (aircraft and ship design) Epidemiology Drug discovery (modeling target protein,

designing drug molecule itself, and modeling interaction)

Chemistry (classical molecular dynamics of molecules and quantum calculations of structure and molecular properties)

Examples

WebMO is web-based ‘front-end’ that makes interaction with Gaussian and other research-grade computational chemistry tools easier.◦ Used for doing quantum mechanics, such as viewing

molecular orbitals Doesn’t actually do calculation

◦ Prepares input file◦ Submits job to ‘engine’ (e.g. Gaussian)◦ Sifts through output file

Created at Hope by Dr. Will Polik◦ www.webmo.net◦ Used in many research labs worldwide in addition to

classrooms◦ Free version available. We will use fancier pay version

Provided by MU3C

What is WebMO?

Login to WebMO running on cluster via web browser on your PC (anywhere)◦ https://mu3c.chem.hope.edu◦ Login: harpercreek2 Password: gobeavers

Build molecule and tell WebMO what you want to know (anywhere)

WebMO creates proper input file and submits job to cluster’s queuing system (cluster)

Cluster runs difficult QM calculation (cluster) WebMO collects results and displays (some

of) them beautifully in your browser (anywhere)

WebMO Process