Workshops
If you are a student, researcher, or staff at Texas A&M University and would like to
receive e-mail notification about upcoming workshops, please send an e-mail to
Lisa M. Pérez with a subject of Subscribe to Workshop list.
If you would like to
stop receiving e-mail notification about upcoming workshops, please send an e-mail to
Lisa M. Pérez
with a subject title of Unsubscribe to Workshop list. (note: this option will not work if you are on a departmental list-serv that the LMS uses for workshop announcements.)
Unix/Linux Workshop
The unix/linux workshop is designed to teach a user the basic commands necessary to work in a unix/linux environment and consists of a 2 1/2-hour lecture, and a 3-hour hands on exercise session.
This workshop is a pre-requisite for all other workshops and required to obtain an account on the unix systems available through the LMS, unless you have a STRONG background in unix or linux.
This workshop is normally offered once during the Fall, Spring, and Summer sessions.
The workshop will include the following topics:
- A brief introduction to the unix/linux operating system
- logging into a unix/linux machine
- basic unix/linux commands
- how to create and edit files (vi and nedit)
- how to compress/store files/directories (gzip and tar)
- how to set up configuration files (.bashrc, .tcshrc, .cshrc, etc)
- remote logins (telnet/ssh)
- transfering files between two unix/linux machines (ftp/sftp)
To receive credit for the unix/linux workshop, you will need to attend the lecture and successfully complete the exercise session.
The last unix workshop was offered in June, 2008 and had 78 participants from 13 different departments:
Atmospheric Sciences, Biochemistry & Biophysics, Biology, Chemical Engineering, Chemistry, Civil Engineering, Cyclotron Institute, Department, Materials Science and Engineering, Mechanical Engineering, Ocean Engineering, Petroleum Engineering, Physics, and Veterinary Integrative Biosciences.
Molecular Modeling Workshop
Download Molecular Modeling Workshop Lecture Slides from June 20th, 2008 (File size 17 MB)
The molecular modeling workshop is designed to teach a user the fundamental principles and concepts of molecular modeling with an emphasis on molecular mechanics/dynamics.
Pre-requisite: Completion of the unix workshop (lecture and lab) or a solid background in unix.
The molecular modeling workshop consists of a 3 hour lecture with a 15 minute break and a 3 hour hands-on exercise session. This workshop is generally offered 1-2 times a year.
The molecular modeling lecture will include the following topics:
- A brief introduction to molecular modeling
- Visualization/Rendering
- Computational Chemistry
- ab initio, density functional theory (DFT), semi-empirical - (brief)
- molecular mechanic (MM)
- molecular dynamics (MD)
- Monte Carlo (MD)
- Informatics
- Illustrative applications of molecular modeling
Exercises for the following programs will be available during hands-on sessions offered with this workshop:
- AMBER
- Mainly for those interested in performing molecular dynamics calculations on biomolecules.
- Cerius 2 software by Accelrys Inc. (formerly MSI)
- Mainly for those interested in the materials science but also applicable for those interested in life sciences
- Insight II software by Acclerys Inc.
- Mainly for those interested in the life sciences and for those interested in using CHARMm
- Macromodel software by Schrodinger Inc.
- A molecular mechanics/dynamics software package. Mainly used for performing monte carlo molecular dynamics simulations.
- Quanta software by Accelrys Inc.
- Mainly for those interested in advanced tools for macromolecular X-ray crystallography.
- Spock by Dr. Jon A. Christopher
- Mainly for those interested in molecular graphics.
The last Molecular Modeling workshop was offered in June of 2008 and had 43 participants from 12 departments.
The next Molecular Modeling Workshop will tentatively be offered in Fall '08
Recommended Molecular Modeling books:
- Guy H. Grant and W. Graham Richards "Computational Chemistry" Oxford University Press, 1995.
- Andrew R. Leach "Molecular Modelling: Principles and Applications" 2nd edition, Prentice Hall 2001
- Chris Cramer "Essentials of Compuational Chemistry: Theories and Models" John Wiley & Sons, 2002.
- David Young "Computational Chemistry: Applying Compuational Techniques to Real-World Problems" John Wiley & Son 2001
- Frank Jensen "Introduction to Computational Chemistry" John Wiley & Son 1999
Quantum Mechanics Short Course
The Quantum Mechanics short course is generally offered in July. It is designed to teach the student how to use the quantum chemistry code Gaussian 03 to model
small - medium size molecules (up to approx. 200 atoms) and the theory behind the calculations. The course is 5 weeks in length and has 15 1-hour lectures and 15 lab assignments (optional).
This course can be time-intensive therefore, during registration an e-mail will be sent to your advisor requesting if he/she wishes you to attend.
Pre-Requisites: Completion of the Unix/Linux Workshop or an extensive background in Unix or Linux.
Suggested reference book:
I strongly suggest that you purchase the book "Exploring Chemistry with Electronic Structure Methods" by J.B. Foresman and A. Frisch. This book is easy to read and written for
the users of the Gaussian code and is inexpensive (softcover: $42 and $30 if you are a student). Most of lecture material and lab exercises will be covered in this text. You can purchase it at the Gaussian web
site ( http://www.gaussian.com/allbooks.htm.
Other suggested books: "Modern Quantum Chemistry:
Introduction to Advanced Electronic Structure Theory" A. Szabo and
N.S. Ostlund. This is a good reference for the mathematics behind the
various methodolgies and is inexpensive ($13.95 Dover).
A good overview of Computational Chemistry would be a new book by David Young entitled
"Computational Chemistry" but it is very expensive (over $100).
Tentative outline for the material covered in this course. All calculations will be performed using the suite of programs
in Gaussian03 (G03) and the graphical interface GaussView.
- Theories covered in this course
- Molecular Mechanics
- Semi-Empirical
- Ab Initio
- Hartree-Fock (HF)
- Moller-Plesset (MP)
- Coupled-Cluster (CC)
- Configuration Interaction (CI)
- Multi-Reference
- Complete Active Space Self Consistent Field (CASSCF)
- Density Functional Theory
- Types of calculations covered in this course
- Single Point Energies
- Geometry Optimization
- reactants
- products
- intermediates
- transition states
- Frequency Calculations
- Intrinsic Reaction Coordinate (IRC)
- Excited state
- solvation models
- Basis Set Superposition Error (BSSE)
- QM/MM Calculations
The last QM Short Course was offered in July of 2008 and had 40 participants from 5 different departments.
CHARMm Workshop
Under Construction
Links to Workshops From Other Sources
Accelrys Inc.
Accelrys Inc. offers workshops for their life science software in Cerius2
and Insight II. For a listing of all workshops and their registration fee, please visit
http://www.accelrys.com/events/training/
Gaussian Inc.
Gaussian Inc. offeres workshops for their electronic structure program - Gaussian 03. Please visit
http://www.gaussian.com/events_top_level.htm for more information.
Super Computing Facility at TAMU
The supercoputing facility at TAMU offeres a number of workshops geared to help users of the super computers available at
TAMU. Please visit http://sc.tamu.edu/shortcourses/ for more information.
