A New Time-Reversible Integrator for Molecular Dynamics Applications

We propose explicit symplectic integrators of molecular dynamics (MD) algorithms for rigid-body molecules in the canonical and isothermal-isobaric ensembles. We also present a symplectic algorithm in the constant normal pressure and lateral surface area ensemble and that combined with the Parrinello-Rahman algorithm. Employing the symplectic integrators for MD algorithms, there is a conserved quantity which is close to Hamiltonian. Therefore, we can perform a MD simulation mo...

The method of choice for integrating the equations of motion of the general N-body problem has been to use an individual time step scheme. For the sake of efficiency, block time steps have been the most popular, where all time step sizes are smaller than a maximum time step size by an integer power of two. We present the first successful attempt to construct a time-symmetric integration scheme, based on block time steps. We demonstrate how our scheme shows a vastly better lon...

At a fundamental level most physical equations are time reversible. In this paper we propose an integrator that preserves this property at the discrete computational level. Our simulations can be run forward and backwards and trace the same path exactly bitwise. We achieve this by implementing theoretically reversible integrators using a mix of fixed and floating point arithmetic. Our main application is in efficiently implementing the reverse step in the adjoint method used ...

Classical molecular dynamics simulations are based on solving Newton's equations of motion. Using a small timestep, numerical integrators such as Verlet generate trajectories of particles as solutions to Newton's equations. We introduce operators derived using recurrent neural networks that accurately solve Newton's equations utilizing sequences of past trajectory data, and produce energy-conserving dynamics of particles using timesteps up to 4000 times larger compared to the...

We present a time-reversible Born-Oppenheimer molecular dynamics scheme, based on self-consistent Hartree-Fock or density functional theory, where both the nuclear and the electronic degrees of freedom are propagated in time. We show how a time-reversible adiabatic propagation of the electronic degrees of freedom is possible despite the non-linearity and incompleteness of the self-consistent field procedure. Time-reversal symmetry excludes a systematic long-term energy drift ...

The implementation of multi-stage splitting integrators is essentially the same as the implementation of the familiar Strang/Verlet method. Therefore multi-stage formulas may be easily incorporated into software that now uses the Strang/Verlet integrator. We study in detail the two-parameter family of palindromic, three-stage splitting formulas and identify choices of parameters that may outperform the Strang/Verlet method. One of these choices leads to a method of effective ...

In the simulation of biological molecules, it is customary to impose constraints on the fastest degrees of freedom to increase the time step. The evaluation of the involved constraint forces must be performed in an efficient manner, for otherwise it would be a bottleneck in the calculations; for this reason, linearly-scaling calculation methods have become widely used. If integrators of order higher than 2 (e.g. Gear predictor-corrector methods) are used to find the trajector...

We present a set of second-order, time-reversible algorithms for the isothermal (NVT) molecular-dynamics (MD) simulation of systems with mixed hard-core/continuous potentials. The methods are generated by combining real-time Nose' thermostats with our previously developed Collision Verlet algorithm [Mol. Phys. 98, 309 (1999)] for constant energy MD simulation of such systems. In all we present 5 methods, one based on the Nose'-Hoover [Phys. Rev. A 31, 1695 (1985)] equations o...

In this note we approach the classical, Newtonian, gravitational $N$-body problem by mean of a new, original numerical integration method. After a short summary of the fundamental characteristics of the problem, including a sketch of some of its mathematical and numerical issues, we present the new algorithm, which is applied to a set of sample cases of initial conditions in the `intermediate' $N$ regime ($N=100$). This choice of $N$ is not due to algorithm limitation but jus...

Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body problem of atoms$-$it computes movements of atoms according to Newtonian physics and empirical descriptions of atomic electrostatic interactions. These simulations require high performance computing resources, as evaluations within each step a...