ИСТИНА

A numerical algorithm for restoring the atomistic structure of poly(lactic acid) (PLA) has been developed and tested. The algorithm restores the atom positions based on A-graft-B coarse- grained representation of PLA [1], where the A beads represent the atoms of the PLA backbone and the B side pendants represent the methyl groups of the PLA. The atomistic structure is composed from pre-defined monomer-size templates. Adjustment of the atomic positions by affine transformation of the templates is performed to reduce the position discrepancy between the coarse-grained configuration and the resulting all-atom structure. After the initially created all-atom configurations undergo energy minimization using standard GROMACS tools they can be used for all-atom simulations. The testing of the algorithm included a reverse mapping of the coarse-grained systems converted from all-atom simulations as well as the systems initially created in coarse-grained representation. It has been shown that the energy parameters of the reverse-mapped systems are identical to those of the initial atomistic simulations within a margin of error. The characteristic equilibration time of the reverse-mapped systems is 0.1 microsecond, which is much less than the timescale of the processes requiring coarse-grained simulations [2]. The algorithm can be used both in multi-scale simulations of PLA and other polyesters as well as for creating initial all-atom configurations of PLA chains with desired parameters, such as elongation, secondary structure, etc. It is particularly useful for multi-scale computer simulation studies of time-consuming processes of mechanical deformation and diffusion. 1. M. Glagolev, A. Glova, D. Mezhenskaia, S. Falkovich, S. Larin, V. Vasilevskaya, S. Lyulin. J. Pol. Sci. B, 2018, 56, 604-612 2. M. K. Glagolev, V. V. Vasilevskaya. Supercomputing Frontiers and Innovations, 2018, 5, 103-106 The research has been supported by RFBR grant number 17-03-00742. Keywords: multiscale simulation, molecular dynamics, poly(lactic acid)