ppt课件-‘tisnotfollytodreamusingmoleculardynamicstosolve.pptVIP

‘Tis not folly to dream: Using Molecular Dynamics to Solve Problems in Chemistry Christopher Adam Hixson and Ralph A. Wheeler Dept. of Chemistry and Biochemistry, University of Oklahoma Classical Problems in Computational Chemistry Geometry Optimization Finding the “best” shape of a molecule Requires finding the minimum on an energy surface Free Energy Calculations Can be used to determine the “spontaneity” of a process Current methods require averaging a large amount of data Molecular Dynamics (MD) is a powerful tool r(t) = r(0) + t v(t) + t2 a(t) For perfect MD, we need to know velocities and accelerations for all time. Must settle for approximation, using discrete algorithm. Applying MD to geometry optimizations If constant temperature MD is used, Boltzmann distribution applies, P ~ exp(- b E), b is an expression of the temperature as an energy Low energy states more probable! Applying MD to calculate free energy differences (Free Energy Perturbation Method) Free energy perturbation (FEP) can use averages from MD to approximate statistical mechanical integrals. Mean Field Methods Reduce Energy Barriers Mean field methods break equations of motion, but reduce energy barriers. Done by “copying” a small part of system, and force felt by rest is average of copied parts. The EXACT approximation EXACT (Ensembles Extracted from A Coordinate Transformation) is a way devised by our group (Hixson, Wheeler, in preparation) to interpolate between conventional and mean field MD. Works by a coordinate transformation, so that the average coordinate (used in mean field methods) becomes main coordinate used in dynamics, other coordinates only used when important. Method intended to provide an alternate technique to solve the geometry optimization problem. Ensemble Free Energy Perturbation Method (EFEP) Uses same coordinate transformation in EXACT to solve an alternate FEP-like equation. Uses either constraint or restraint to keep uncopied parts of system