COMP 380 |
| Two simple models are developed to accurately account for the solvation effects in molecular dynamics simulations of biomolecules. The methods reduce the amount of solvent that must be treated explicitly to one or two solvation shells, significantly reducing the computational complexity. In the dynamic boundary model, a confining potential is imposed on the solvent, that responds dynamically to the fluctuations in solvent distribution and biomolecular conformations. In pseudo-periodic boundary solvation model, surface solvent molecules are allowed to exchange via a translational shift to its ‘image' position akin to the periodic boundary condition simulation. In both models, long range solvation effects are treated via a Poisson-Boltzmann continuum dielectric method. The models are applied to simulations of a 9 residue polyalanine helix. Comparison of various structural properties with those computed from conventional periodic boundary condition simulations show excellent agreement. |
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Current Techniques in Molecular Simulation of Biological Systems
9:00 AM-11:55 AM, Wednesday, August 22, 2007 BCEC -- 156B, Oral
Division of Computers in Chemistry |