Speaker
Martin Petrek
(CESNET)
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 the 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.
Summary
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).
Author
Martin Petrek
(CESNET)
Co-authors
Jan Kmunicek
(CESNET)
Petr Kulhanek
(CESNET)
