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The free energy profiles for proton transfer along the oriented water file inside the gramicidin A channel were calculated. An original implementation of the rigid-body molecular dynamics method was used for describing the peptide groups of the channel and outer water molecules. The inner water wire was simulated using the PM6 force field parameters, which adequately describe the formation and cleavage of chemical and hydrogen bonds in water molecules. Different mechanisms of proton transfer through the gramicidin A channel were considered, namely, proton H+ translocation, transfer of the anion defect OH−, and reorientation of the water file inside the channel. To facilitate parallel calculations of trajectories, the reaction coordinate was divided into segments, and the results were combined by the weighted histogram analysis method. The first two processes, H+ and OH− transfers, were shown to be barrierless. Only the stage of reorientation of the water file inside the channel has an energy barrier.

We describe an implementation of the replica-exchange molecular dynamics (REMD) algorithm for rigid-body molecular dynamics targeting its application in the flexible effective fragment quantum mechanical–molecular mechanical (QM/MM) method. The main objective of the stage of the project is to obtain an efficient minimization tool for the MM subsystem. The computer program developed allows one to carry out calculations of molecular dynamics trajectories for atomic particles and for rigid bodies at constant temperature, using the chain Nose–Hoover thermostat. For REMD calculations, the OpenTS dynamic parallelization is used, which allows one to run simulations either on single computational clusters or on meta-clusters. A two-level parallelization scheme has been implemented, assuming that both REMD (upper level) and individual molecular dynamics trajectories (lower level) are parallelized. Structures of small and large water clusters as well as protein conformations are considered as first applications. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006

We describe a new implementation of the molecular dynamics method aimed at simulation of the properties of biomolecular systems in which chemical reactions are possible. The quantum mechanical/molecular mechanical method based on the effective fragment potential theory is used for calculating the energies and forces along trajectories. Due to specific features of the effective fragment theory, the behavior of the molecular mechanical subsystem is described by rigid body dynamics. The method has been applied to simulation of proton transfer along the chain of water molecules inside the gramicidin channel.

Based on molecular dynamics simulations of nanocars with fullerene wheels on the surface of an Au (110) gold crystal, estimates of diffusion coefficients are reported.