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The
research projects in the Simmerling lab require powerful computers in
order to obtain precise data for a fairly complex energy function. Our
group is one of the core development teams for the Amber package, which
we use for most of our simulations. Visualization is typically
performed using programs such as VMD or MOIL-View. Since calculations
on large biomolecular systems are very computationally demanding, we
use supercomputer resources at the NSF-funded national centers. In
particular, a large fraction of our work is generated at NCSA, which
has excellent hardware along with an outstanding support team. The SGI
computer company has also donated computer time that has been very
valuable for our work.
Software development
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Amber package for molecular simulation
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Moil-view (molecular visualization program for SGI workstations)
Computer resources
Other software that we use extensively
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Computational
Structural Biology
The
goals of a computational chemist are to accurately simulate known
properties of
molecules, assist in the refinement and interpretation of experimental
data and
predict the results of future experiments. While quantum mechanical
methods can
be highly accurate, they are limited in that they currently cannot be
applied
to large systems such as proteins and nucleic acids, and little or no
explicit
solvent can be included in the calculations. Since the research in my
lab
involves relatively large biomolecular systems (such as proteins and
nucleic
acids) where specific interactions with solvent molecules are often
important,
we use the methods of molecular mechanics. Typical calculations involve
molecular dynamics of the molecule of interest along with thousands of
explicit
solvent molecules, where the behavior of the molecule as a function of
time is
used to determine kinetic and thermodynamic properties of the system.
These
simulations can provide an atomic-detail picture of the behavior of a
single
molecule, rather than the time- and ensemble-averaged views that come
from most
experiments.
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