Computational Chemistry Center

The computational chemistry cluster has been created to promote the use of theoretical methods in research of the traditionally experimental groups, and to foster collaborations between experimental and theoretical groups of the department.

The facilities consist of a CPU/GPU computational cluster named Chembeast sponsored by the funds from the departmental chair and generous contributions by a number of faculty members: Ronchao Jin, Alex Guo, Michael Hendrich, Linda Peatanu, Danith Li and  Subha Das.

We accept contributions for cluster on-going support and expansion in $500 increments. Once the project gains enough momentum we will apply for external funding.


The cluster is  open  for use by all experimental groups of the department. The cluster is hosted in the Theory Suite. It is accessible remotely and it also has two open space graphical terminals.

Kurnikova group provides support and oversees administration of the cluster, tutoring of the new users, and is open to collaborations on bio-molecular applications.

Please contact Maria to express interest and discuss your needs.


In the first year of cluster operation it proved a success and a welcome addition to the departmental shared resources.

Several research groups have been using the facility and a number of new collaborations to incorporate computational chemistry in the on-going experimental projects were initiated:

  • A. Guo and M. Kurnikova collaboration has resulted in a recent publication  In this paper computational chemistry was used to distinguish between two possible arrangements of a ligand in the enzyme binding site
  • An ongoing collaborative project S. Das, L. Peteanu and M. Kurnikova aims to apply molecular dynamics simulations to help interpret spectroscopic data on protein RNA interactions
  • Computational chemistry is used to help D. Li with the design of novel nucleotides by computing the probability of enantiomers in proposed novel bases.
  • S. Sydlic is using the cluster to compute how polymers of different length acquire and relieve stress
  • T. Kowalewski uses the cluster to perform DFT calculations

Hardware

 


Software

 currently has a number of standard computational chemistry and molecular modeling software packages installed.

See software List for the list of available software


Instructions, Tutoring, Teaching

Please find here short instructions for the new users.

In the fall semester we will be offering tutorial sessions for cluster access, unix primer and running standard software, such as Gaussian and AMBER

The course 09-560 on Molecular Modeling and Computational Chemistry offered in the Spring semester  provides a beginner user introduction to methods of computational chemistry and practical training for using the software on windows PC and Unix machines.