Symbiose Project Team - INRIA/Irisa © 2007 - 2008


6 Mai: Michel Masella (Dir. des Sciences du Vivant, CEA/DSV/iBiTEC-S/SIMOPRO/LCV, Gif-sur-Yvette)
Written by Pierre PETERLONGO   

An accurate and efficient computational approach to investigate proteinic systems in aqueous solution at the atomic scale.

10h30 Salle Aurigny

 

The dynamic coupling between a polarizable protein force field and a particle-based implicit
solvent model will be described. The polarizable force field, TCPEp, developed recently to simulate
protein systems, is characterized by a reduced number of polarizable sites, with a substantial gain in
efficiency for an equal chemical accuracy. The Polarizable Pseudo-Particle (PPP) solvent model
represents the macroscopic solvent polarization by induced dipoles placed on mobile Lennard-Jones
pseudo-particles, whose parameters have been recently refined to reproduce the main energetic and
structural properties of cavity hydration. The solvent induced dipoles are sensitive to the solute
electric field, but not to each other, so that the computational cost of solvent-solvent interactions is
basically negligible. This approach allows one to perform a nanosecond scale molecular dynamics
simulation of a 60-residues protein in about 9h, using a MPI version of our POLARIS(MD) code on
4 recent processors. Application of this approach will be presented.

 


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