Massively Parallel implementation of the Steered Molecular Dynamic in Tinker-HP for polarizable and non-polarizable force fields

Frédéric Célerse
Laboratoire de Chimie Théorique - UMR7616 UPMC & CNRS, Paris, France
Jeudi 8 Novembre 2018, 11h00
bibliothèque LCT, tour 12 - 13, 4^ème étage

Steered Molecular Dynamics (SMD) is a powerful methodology to accelerate rare events occurring in a Molecular Dynamics (MD) by applying an external force to a set of chosen atoms [1]. While SMD provides non-equilibrium trajectories, it is of a main interest to be able to reconstruct equilibrium properties such as Potential of Mean Force (PMF) [2,3]. To be able to use multiple distributed polarizable force fields (such as AMOEBA), the methodology has been implemented in the Tinker-HP software [4]. The SMD implementation has been firstly compared to NAMD, considered as a reference [1]. We further tested it with different type of force fields (polarizable and non-polarizable) with use of systems of different size. Polarization effect has been isolated and characterized by a decrease of the free energy barrier of the PMF compared to non-polarizable force fields in most of the cases.

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References :
[1] J. C. Phillips, R. Braun, W. Wang et al., J. Comput. Chem. B 2005, 26, 1781.
[2] S. Park, F. Khalili-Araghi, E. Tajkhorshid, and K. Schulten, J. Chem. Phys. 2003, 119, 3559.
[3] S. Park and K. Schulten, J. Chem. Phys. 2004, 120, 5946.
[4] L. Lagardère, L.-H. Jolly, F. Lipparini et al., Chem. Sci. 2018, 9, 956.