Molecular dynamics - non-equilibrium candidate Monte Carlo simulations (MD/NCMC) is a newly designed method aiming to design Monte Carlo moves with high acceptance probabilities that also rapidly sample uncorrelated configurations. Currently, hybrid MD/NCMC methods use pre-defined states and transition paths, which limit their usages. In this study, a MD/NCMC scheme with coarse-grain (CG) model guided move is proposed and studied. The new method generates the correct distribution, and is up to eight times faster than a brute force MD method. During the hybrid simulation, standard MD and MC switch is performed alternatively. During the MC switch, a coarse-grained (CG) model for the current system is first built. The CG system is then freely propagated without additional constrain. The simulation is stopped when the certain stopping criterion is met. The target values for the chosen reaction coordinates are then extracted from the new CG system, and used to constrain the fine-grained system during the constrained MD simulation. At the end, the energy difference is calculated and used in metropolis criterion to decide if the new conformation is accepted. The new method generates the exact same distribution and increase diffusion constant by 80 times in a twelve atom model system. The method is also tested on tri-, penta-, deca-alanine and (AAQAA)3. The distributions of phi/psi angle and distances/ angles of carbon-alpha are all compatible with experimental results available and brute force MD simulation results. The efficiency of the method is measured by the frequency of system jumping between different conformation regions, including extended alpha-helix, beat-sheet, ppII, left-handed alpha-helix. For all four systems, the efficiency of the method is around eight times faster than the pure MD simulation. In a particular simulation of (AAQAA)3, the distributions converge within 60ns of simulation for when starting with either alpha-helix or beta-sheet structure.

New efficient hybrid MD/MC scheme with CG-guided move and non-equilibrium switch

248th National Meeting (2014)

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