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BEMuSE overview.

by Riccardo Di Meo last modified 2007-11-21 21:02

Bias-Exchange Metadynamics Submission Environment: a short introduction to the physical problem.

Overview

Protein folding is well-known in the HPC community as an extremely hard computational task: this is due to the need to sample a huge number of metastable conformations of a polypeptide chain, characterized by a large number of degrees of freedom, until the experimental folded state is reached.

Most of the existing approaches to protein folding speed-up the exploration of the conformation space by oversimplifying the description of the forces between atoms, to the point of treating the solvent in a continuous (implicit) way, at the expense of the accuracy and predictability of the results.

The Bias-Exchange Metadynamics technique, recently developed by Alessandro Laio and Stefano Piana [ref 1], allows instead for both fast and accurate results: detailed thermodynamic and kinetic informations on the folding process are obtained at a cheap computational cost, sheding light on experiments.

The Trp-cage (20 amino acids) and Advillin (36 amino acids) proteins have been reversibly folded in explicit water using 8 parallel simulations of only 40 ns each. See the following articles for references:

  • S. Piana and A. Laio, J. Phys. Chem. B 111, 4553 (2007).
  • S. Piana, A. Laio, F. Marinelli, M. Van Troys, D. Bourry, C. Ampe, and J. C. Martins, J. Mol. Biol. (in press).

After we came in contact with the group of Alessandro Laio it appeared immediately clear how much the algorithm would had benefit from the GRID and we asked ourselves if the porting of such method to the EGEE infrastructure was feasible, and if so, which kind of performances we could expect from it.

In this section we will present our results in porting the application from it's original context (a plain MPI enabled application), explaining in detail the problems we faced and the ways we solved them, the results obtained and a small tutorial/guide to the software developed.

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