Welcome to the Computational Chemistry Lab

The lab consists of a Beowulf cluster, several graphics workstations, along with assorted printers, storage devices, etc:

Little Giant , the 32 node parallel computer. chem, a quad-processor server, is name of the 'master' node that is seperate from the 57 'slave' nodes. The slaves have the names lg1 to lg57, all nodes higher than 32 are dual processor nodes.

Files on any of these computers can be accessed from any other computer through the '/v' file system. For example, to access files on lg1 from chem, they can be reached from '/v/lg1/...'. On the same note, files from chem can be accessed from lg1 from '/v/chem/...'

Here's a list of the software, and descriptions, installed on the computers.

Before You Get Started...

All these machines run the Linux operating system, a version of UNIX. Click here for a brief introduction to some of the basics of using these operating systems, or here for the official online Red Hat Linux documentation. The brief introduction here gives the basics, and should be adequate for people who just want to know how to get around in the file system, while the official online documentation gives more complex commands for working with files. Yet another linux tutorial can be found here .

Using CHARMM

CHARMM Documentation
An introduction to CHARMM tutorial using water molecules.
Another CHARMM Tutorial using butane molecules. This introduces Gnuplot and VMD.
A CHARMM tutorial and an introduction to CHARMM data structures from Krzysztov Kuczera at the University of Kansas.
A CHARMM tutorial from Roland Stote that also includes excellent background material on MD simulation.