Grid Computing for Long Time Propagations in Molecular Dynamics of Biomolecules and Extended Phase Space Sampling

Scientists from Department of Chemistry, University of Crete (UoC) and 
Institute of Electronic Structure and Laser, 
FOundation for Research and Technology Hellas (FORTH)  have used the HellasGrid Infrastructure and the EGI Grid infrastructure in order to solve problems coming from the area of Computational Chemistry.

More specific, the scientists made studies on dynamics and spectroscopy of proteins and other biomolecules, enzymatic reactions, and free energy hypersurface calculations for protein – ligand interactions by integrating very long time trajectories and making extended sampling of the classical phase space [1-3].

For problems which exhibit ergodicity in a submanifold of the phase space manifold of the system, time averages are converted to phase space averages, and thus to high throughput problems. The algorithm that have been developed is based on the principle to run short jobs, store intermediate results, and resubmit the jobs as many times as needed to achieve a predetermined total integration time [1]. This approach cures shortcomings of the current productive Grid.

The production of a free energy hypersurface, requires one to run thousands or even millions of jobs, a task which can be fulfilled if thousands of CPUs are available in a reasonable amount of time [2,3]. Scripts based on the gLite middleware have been developed and tested at the HellasGrid and EGI infrastructure which can handle such tasks.

Quantum molecular dynamics for intermediate size biomolecules require a interoperability of high throughput and high performance computing. This is scientists’ plan for solving problems involving proton-coupled electron transfer (PCET), which are encountered in enzyme reactions, fuel cells, chemical sensors and electrochemical devices.

Contact details

Members of the Theoretical and Computational Chemistry group in Crete (TCCC):

  • Prof. Stavros C. Farantos, Theoretical and Computational Chemistry, farantos (at) iesl.forth.gr
  • Mr. Manos Giatromanolakis, IT Manager and Systems Analyst, gmanos (at) iesl.forth.gr
  • Prof. Vangelis Daskalakis, Computational Biochemistry, chem487 (at) edu.uoc.gr
  • Dr. Osvaldo Gervasi, Computer scientist, administrator of Compchem Virtual Organization,  osvaldo (at) unipg.it
  • Dr. Massimiliano Porrini, Theoretical and Computational Chemistry, maxp (at) iesl.forth.gr
  • Dr. Jaime Suarez, Theoretical and Computational Chemistry, jaime.suarez (at) iesl.forth.gr

References

  1. V. Daskalakis, M. Giatromanolakis, M. Porrini, S. C. Farantos, and O. Gervasi, Computer Physics, Chapter: Grid computing multiple shooting algorithms for extended phase space sampling and long time propagation in Molecular Dynamics, Nova Science Publishing Co., 2011.
  2. M. Porrini, V. Daskalakis, and S. C. Farantos, Thermodynamic Perturbation Calculations on Cytochrome c Oxidases interacting with small ligands, Phys. Chem. Chem. Phys., submitted, 2011.
  3. Massimiliano Porrini, Vangelis Daskalakis, S. C. Farantos, and Constantinos Varotsis, Heme Cavity Dynamics of Photodissociated CO from ba3-Cytochrome c Oxidase: the Role of Ring-D Propionate, J. Phys. Chem. B, 113(35):12129-12135, 2009.