Publication details

Computational Chemistry Achievements within VOCE Environment



Year of publication 2006
Type Article in Proceedings
MU Faculty or unit

Faculty of Science

Web EGEE'06
Field Macromolecular chemistry
Description This contribution describes accomplishments achieved by the computational chemistry community utilizing computational resources and corresponding applications within a grid environment of the Virtual Organization for Central Europe (VOCE). VOCE infrastructure, part of the EGEE II Grid, currently consists of computational resources and storage capacities provided by the Central European resource owners. VOCE currently provides a complete grid infrastructure running all necessary grid services helping thus scientists to solve their research projects and problems. One of the currently intensively studied areas of modern material design and drug discovery is chemistry of interlocked supramolecules and their mutual interactions. In the presented work, we investigate rotaxane, a supramolecular complex. Rotaxanes are interlocked molecules in which macrocycle (the 'wheel') is threaded by a long 'axle' component. Our system consists of a molecule cucurbit[7]uril (CB7) and a 4,4'-bipyridinium derivate. Experiments show a switch-like movements along the axle in this supramolecular complex. To give a detailed insight to the switch-mechanism we calculated the free energy profile along reaction coordinate related to this movement. The evaluation of the free energy is a computationally demanding task requiring extensive computational resources due to necessity to properly sample large phase-space. Currently used methods for the free energy estimations (such as umbrella, bluemoon or adaptive biassing force method) require a calculation of a huge amount of middle-length molecular dynamic simulations which can run independently in parallel. Therefore, these types of computational tasks are very well suited to exploit large grid environments like the VOCE. The complete solving of described research problem comprises approximately hundreds thousands of CPU hours at 1.6 GHz CPU with 1 GB RAM. Our results clearly demonstrate that the VOCE Grid is the place where challenging applications requiring advanced computational chemistry techniques can be easily utilized and corresponding research problems successfully solved.
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