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Current Research
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Biochemistry
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The most fundamental description of biological systems is
computed using quantum mechanics, with molecular mechanics
and molecular dynamics progressively simplifying
the calculations to allow dynamics simulations on protein
systems. One of the advantages of molecular dynamics
simulations is that correlations between motions can be
disentangled, a phenomenon that is obscured in experiments
on ensembles.
The molecular systems that the researchers are interested in
allow for ultra-high resolution X-Ray data in combination
with a broad spectrum of functional assays. They are interested
in a combination of structural work in concert with
biochemical characterization which is completed by highperformance
computations. |
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Although experiments can determine
what is moving and how fast, molecular dynamics
simulations can answer why things move, because the underlying
forces and corresponding energies are included in
the simulation. The resultant predictions inspire new experiments,
forming part of a combined effort to solve the
puzzle of how proteins work.
The research into the dynamics of large biological molecules
requires extensive computational resources. West-
Grid has been an essential resource for computation in
terms of both the accessibility of the
software that researchers require for
their work, and in that it has streamlined
their molecular dynamics calculations.
The GROningen MAchine
for Chemical Simulations (GROMACS) that they
require is a globally ecognized molecular dynamics
software package that is installed on most
WestGrid machines in its most recent version,
with the ability to utilize up to the last few versions
due to compatibility issues with laboratory
computers.
Generating a single molecular dynamics trajectory
2ns in length is 5GB in size, and, depending
on the number of accessible processors, can take
days to complete.
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Jobs on WestGrid machines
can be run with up to 64 processors, significantly
reducing the total computation time Additionally,
having permission to run a number of separate
simulations on a single machine, and having
access to a number of machines greatly speeds up
the time required to complete a project.
WestGrid’s large storage facilities (Silo, Gridstore)
make it easy to store data for future use.
The recent addition of Bugaboo is ideal for these
memory intensive projects, since this machine
allows researchers to access 1 TB of storage for
works in progress. |
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