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Nanopores

Mechanisms of Phase Transformations of TiO2 Nanotubes and Nanorods

Andrei Buin, Styliani Consta*, and Tsun-Kong Sham
Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7
J. Phys. Chem. C, 2011, 115 (45), pp 22257–22264

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 www.gromacs.org 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 9444a-Computer Simulations in Chemistry

THE UNIVERSITY OF WESTERN ONTARIO
DEPARTMENT OF CHEMISTRY
CHEMISTRY 9444A-FALL 2010

CHEM 9444a-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.

Render a molecule from command line using VMD

export name="1hjm"
export tachyon="/usr/local/lib/vmd/tachyon_LINUX"

Create script using VMD

The result

Research

Every attempt to employ mathematical methods in the study of chemical questions must be considered profoundly irrational and contrary to the spirit of chemistry.... if mathematical analysis should ever hold a prominent place in chemistry, an aberration which is happily almost impossible, it would occasion a rapid and widespread degeneration of that science.

Auguste Comte, Cours de philosophie positive, 1830


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