ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics

Discrete approaches for the nonlinear analysis of in plane loaded masonry walls: Molecular dynamic and static algorithm solutions

Calculating the free energy of nearly jammed hard-particle packings using molecular dynamics

We propose a novel molecular dynamics (MD) algorithm for approximately dealing with a nuclear quantum dynamics in a real-time MD simulation. We have found that real-time dynamics of the ensemble of classical particles acquires quantum nature by introducing a constant quantum mechanical uncertainty constraint on its classical dynamics. The constant uncertainty constraint is handled by the Lagrange multiplier method and implemented into a conventional MD algorithm. The resulting constant uncertainty molecular dynamics (CUMD) is applied to the calculation of quantum position autocorrelation functions on quartic and Morse potentials. The test calculations show that CUMD gives better performance than ring-polymer MD because of the inclusion of the quantum zero-point energy during real-time evolution as well as the quantum imaginary-time statistical effect stored in an initial condition. The CUMD approach will be a possible starting point for new real-time quantum dynamics simulation in condensed phase.

ABSTRACTWe introduce a Discard-and-Restart molecular dynamics (MD) algorithm tailored for the sampling of realistic protein transition states. It aids computational structure-based drug discovery by reducing the simulation times to compute transition pathways by up to 2000x. The algorithm iteratively performs short MD simulations and measures their proximity to a target state via a collective variable (CV) loss, which can be defined in a flexible fashion, locally or globally. Using the loss, if the trajectory proceeds toward the target, the MD simulation continues. Otherwise, it is discarded and a new MD simulation is restarted, with new initial velocities randomly drawn from a Boltzmann distribution. The discard-and-restart algorithm demonstrates efficacy and atomistic accuracy in capturing the folding pathways in several contexts: (1) fast-folding small protein domains; (2) the folding intermediate of the prion protein PrP; and (3) the spontaneous partial unfolding of α-Tubulin, a crucial event for microtubule severing. During each iteration of the algorithm, we are able to perform AI-based analysis of the transitory conformations to find binding pockets, which could potentially represent druggable sites. Overall, our algorithm enables systematic and computationally efficient exploration of conformational landscapes, enhancing the design of ligands targeting dynamic protein states.

A discard-and-restart MD algorithm for the sampling of protein intermediate states.

This work describes the software package and algorithms for molecular dynamics using NVIDEA GPU G80, G84, and G92. All potentials needed for MM2 and AMBER force fields are implemented and the combination of different potentials is allowed. The performance comparison of different MD algorithms on GPU and CPU is presented. All software is available from www.gpamm.mntech.ru.

A study of local effect and global effect on the microthermal bio-flows by molecular dynamics

The use of non-Hamiltonian dynamical systems to perform molecular dynamics simulation studies is becoming standard. However, the lack of a sound statistical mechanical foundation for non-Hamiltonian systems has caused numerous misconceptions about the phase space distribution functions generated by these systems to appear in the literature. Recently, a rigorous classical statistical mechanical theory of non-Hamiltonian systems has been derived, [M. E. Tuckerman, et al., Europhys. Lett. 45, 149 (1999)]. In this paper, the new theoretical formulation is employed to develop the non-Hamiltonian generalization of the usual Hamiltonian based statistical mechanical phase space principles. In particular, it is shown how the invariant phase space measure and the complete sets of conservation laws of the dynamical system can be combined with the generalized Liouville equation for non-Hamiltonian systems to produce a well defined expression for the phase space distribution function. The generalization provides a systematic, controlled procedure for designing non-Hamiltonian molecular dynamics algorithms which can be used to generate nonmicrocanonical ensembles, stationary nonequilibrium flows, and/or the dynamics of constrained systems. In light of this new general analysis, molecular dynamics algorithms for the canonical and isothermal–isobaric ensembles are examined, potential difficulties are illuminated, and the limitations of previous theoretical treatments are elucidated.

Simulation of point defect diffusion in germanium

An efficient molecular dynamics (MD) algorithm is presented in this paper for biomolecular systems, which incorporates a novel variation on the fast multipole method (FMM) coupled to the reversible reference system propagator algorithm (r-RESPA). A top-down FMM is proposed which calculates multipoles recursively from the top of the box tree instead of from the bottom in Greengard’s original FMM, in an effort to be more efficient for noncubic or nonuniform systems. In addition, the use of noncubic box subdivisions of biomolecular systems is used and discussed. Reversible RESPA based on a Trotter factorization of the Liouville propagator in generating numerical integration schemes is coupled to the top-down FMM and applied to a MD study of proteins in vacuo, and is shown to be able to use a much larger time-step than the standard velocity Verlet method for a comparable level of accuracy. Furthermore, by using the FMM it becomes possible to perform MD simulations for very large biomolecules, since memory and CPU time requirements are now nearly of order of O(N) instead of O(N2). For a protein with 9513 atoms (the photosynthetic reaction center), the efficient MD algorithm leads to 20-fold reduction in CPU time for the Coulomb interaction and approximately 15-fold reduction in total CPU time over the standard velocity Verlet algorithm with a direct evaluation of Coulomb forces.

We investigate granular materials undergoing vibrations, using a molecular dynamics (MD) algorithm, and we display limitations of the numerical method. We show that previously reported convection patterns obtained through MD may be due to the microscopic interactions. MD calculations often use parameters which lead to unphysically large contact times between beads and to large density fluctuations. These in turn enhance the appearance of convection rolls, a numerical finding without experimental counterpart.

A hybrid molecular dynamics (MD) algorithm which combines a full MD description of solute–solute and solute–solvent interactions with a mesoscale treatment of solvent-solvent interactions is developed. The solvent dynamics is modeled on a mesoscale level by coarse graining the system into cells and updating the velocities of the solvent molecules by multiparticle collisions within each cell. The solvent dynamics is such that the correct hydrodynamic equations are obtained in the macroscopic limit and a Boltzmann distribution of velocities is established in equilibrium. Discrete-time versions of the hydrodynamic equations and Green–Kubo autocorrelation functions are derived. Between the discrete-time solvent–solvent collisions the system evolves by the classical equations of motion. The hybrid MD scheme is illustrated by an application to the Brownian motion of a nanocolloidal particle in the mesoscale solvent and concentrated nanocolloidal suspensions.

New approaches to potential energy minimization and molecular dynamics algorithms

Understandingtheadsorption/diffusioncharacteristics of CH4 at low temperatures (<273.15K) is of great significance not only for coal bed methane estimationbut also for gas disaster prevention and methane storage in deep coalbeds. In this work, the adsorption configurations of anthracite macromoleculeswere constructed with Materials Studio, and then, the adsorption anddiffusion behaviors of CH4 at 233.15–363.15 K weresimulated, respectively, using grand canonical Monte Carlo (GCMC)and molecular dynamics (MD) algorithms. The results show that theabsolute adsorption capacities of CH4 at low temperaturesare substantially larger than those at high temperatures, and theadsorption amount further increases with the continued cooling ata given sorption pressure. The isosteric heat of CH4 adsorptionranges from 8.715 to 11.746 kJ/mol, belonging to a spontaneous physicaladsorption. The self-diffusivity Ds ofCH4 at low temperatures is substantially smaller than thatat high temperatures and further decreases with cooling. The mostprobable velocity of CH4 molecules (vp) greatly decreases, and the number of gas molecules witha higher energy is significantly reduced by a low temperature, resultingin the diffusion inhibition of CH4.

Molecular dynamics simulation of shockwaves including some nonadiabatic effects