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Enhanced sampling using multiple interacting replicas in a nonequilibrium regimeAuthor: ABHIRATH BATRA Date: 2019-01-25 Report no: IIIT/TH/2019/12 Advisor:Prabhakar Bhimalapuram AbstractEnhanced Sampling in Molecular Dynamics simulations is one of the main challenges of computational chemistry. The problem arises due to existence of local minima in the free energy landscape, which serve as strong attractors. The problem is tackled by various traditional methods by somehow biasing the walker out of the minima to explore rest of conformational space. In this work we propose a multiple replica method that introduces repulsive interactions between them so as to diverge them in conformational space. These trajectories however follow a time dependent hamiltonian, statistics of which can only we studied in the nonequilibrium regime. We use the landmark work of Jarzynski to put together the statistics from these walkers to reconstruct the equilibrium free energy landscape. We also describe an implementation of the proposed method in the popular MD software, PLUMED so as to facilitate easy usability of the method for the larger community. Full thesis: pdf Centre for Computational Natural Sciences and Bioinformatics |
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