Submitting jobs on the theory cluster

Job Submission

To submit a 4 processor job on the cluster run the following command

qsub -N jobname -pe openmpi 4 submit_gromacs.bash

where submit_gromacs.bash is the following file in your work directory

Molecular modelling tutorial

A live debian system could be installed onto a memory key. Please, provide me with a key and I 'll burn a copy for you. Booting from the memory key you can make few runs without modifying your computer or installing additional software. Otherwise check and install Gromacs on your computer.

In the home directory of the default user styliani you can find an example of MD run using Gromacs package.

Open a terminal window.

~$ cd teaching

Files in the example directory


CHEM 4444a "Computer Simulations in Chemistry" Fall


CHEM 4444a-Computer Simulations in Chemistry

Rare event dynamics and reaction rates

Many processes in chemical and biological systems such as chemical reactions, conformational changes of macromolecules, nucleation processes in solution or in other condensed phases take place by infrequent fluctuations of the locations of the molecules in the solvent and the reactive system. Capturing these special fluctuations that finally determine the mechanism and rate of the process is a challenging problem in computations. This problem lies at the heart of chemistry.

Zhang Hui is leaving for an academic position in China

Group photo

Jun Chung, Daniella Mei, Styliani Constas, Serge Ayissi and Zhang Hui

Molecular simulations of the conformational behavior of 1-chloropropane adsorbed in Faujasite-type zeolite. 4490 project, 2009

The increased awareness of the environmental hazards of chlorinated halocarbons (CHCs) has led to the development of new separation and catalytic conversion processes of CHCs. Faujasite zeolite is the most widely used material in separation processes in petroleum industry and is a candidate for the catalytic decomposition of CHCs. In this project molecular simulations will be performed by inserting molecules of 1-chloropropane in the Faujasite zeolite matrix.

Molecular simulations of diffusion in zeolites. 4490 project, 2009

Diffusion of aromatic compounds in zeolites is significant in petrochemical industry since zeolites are used as catalysts in petrochemical processes. The diffusion in zeolites is also a challenging problem in simulations. The zeolite that will be studied is composed out of oxygen and silicon atoms and it is penetrated by zig-zag and straight channels that intersect. Diffusion takes place along these channels. The challenge in simulations arises from the fact that the free energy profile of the diffusion process along the channels involves several barriers.

Estimation of free energies of binding and changes in conformation by molecular simulations. 4490 project, 2009

The free energy of binding of two molecules is defined as the free energy difference between these molecules in the bound and the free, unbound state. This quantity can be determined experimentally through the measurement of binding constants using for instance BIAcore or microcalorimetry techniques. In simulations several schemes that involve statistical mechanics and reaction paths have been devised in order to compute free energy differences.

Molecular simulations of the disintegration of charged droplets in the presence of macromolecules. 4490 project, 2009

Highly charged liquid droplets that contain solvent and excess of ions of the same sign are ubiquitous in aerosol and atmospheric chemistry, electrospray methods, as well as in technologies such as inkjet-printing and air-purification processes. In analytical chemistry techniques, electrospray methods are coupled to mass spectrometry (ESMS). Electrospray mass spectrometry is often used for the detection of macromolecules such as polypeptides or proteins in solution.


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