Speaker
Dr
Mariusz Sterzel
(Academic Computer Centre "Cyfronet")
Description
The EGEE Grid Project enables access to huge computing and storage resources. Taking
this oportunity we have tried to identyfie chemical problems that could be computed
in this environment. Some of the results considered within this work are presented
with description focused on requirements for the computational enviroment as well as
techniques of Grid-enabling computations based on packages like GAMESS and GAUSIAN.
Recently lots of work has been done in the area of parallelizing the existing codes
and discovering new ones used in quantum chemistry. That allows calculations to run
much faster now than even ten years ago. However, there still exist tasks where
without a large number of processors it is not possible to obtain satisfactory
results. The two main challenges are harmonic frequency calculations and ab-initio
(AI) molecular dynamics (MD) simulations. The former ones are mainly used to analyze
molecular vibrations. Despite the fact that the algorithm for analytic harmonic
frequency calculations has been known for over 20 years, only few quantum chemical
codes have it implemented. The other still use numerical scheme where for a given
number of atoms (N) in a molecule, , and for more accurate calculations
independent steps (energy + gradients) have to be done to get harmonic frequencies.
To achieve this as many processors as possible is needed to fit that huge number of
calculations. This makes grids technology an ideal solution for that kind of
application. The second challenge, MD simulations are mainly used in a case where
’static’ calculation like for example determination of Nuclear Magnetic Resonance
(NMR) chemical shifts gives wrong results. MD consists usually of two steps. In the
first one the nuclear gradients are calculated, in the second one, based on obtained
gradients, the actual classical forces acting on an atom are calculated. Knowing
these forces one can estimate accelerations, velocities and guess new position of the
atom after a given short period of time (so called time step). Finally the whole
process is repeated for every new position of each atom. In case of mentioned NMR
experiment we are interested in the average value of chemical shift over simulation.
Of course NMR calculations are also very time consuming themselves and have to be
done for many different geometries which again makes grid technology an ideal
solution to final NMR chemical shift calculations.
We present here two kinds of calculations. First we show results for geometry
optimization and frequency calculations for a few carotenoids. These molecules are of
almost constant interest since they cooperate with chlorophyll in photosynthesis
process. All the calculations have been done within EGEE Grid (VOCE VO). We also
present an example of MD calculations and share our knowledge about what kind of
problems can be found during such studies.
Authors
Dr
Mariusz Sterzel
(Academic Computer Centre "Cyfronet")
Mrs
Tomasz Szepieniec
(Academic Computer Centre "Cyfronet")
Co-authors
Dr
Leszek Fiedor
(Faculty of Biotechnology, Jagiellonian University)
Dr
Mariusz Pilch
(Faculty of Chemistry, Jagiellonian University)
