https://www.sandia.gov/~sjplimp/papers/jcompphys95.pdf

Fast parallel algorithms for short-range molecular dynamics

Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

/pdf/scalable-molecular-dynamics-with-namd-3j7xyc70g4.pdf

Scalable Molecular Dynamics with NAMD

http://kth.diva-portal.org/smash/get/diva2:1303357/FULLTEXT01

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

We provide the first demonstration that molecular-level methods based on gas kinetic theory and molecular chaos can simulate turbulence and its decay. The direct simulation Monte Carlo (DSMC) method, a molecular-level technique for simulating gas flows that resolves phenomena from molecular to hydrodynamic (continuum) length scales, is applied to simulate the Taylor-Green vortex flow. The DSMC simulations reproduce the Kolmogorov $\ensuremath{-}5/3$ law and agree well with the turbulent kinetic energy and energy dissipation rate obtained from direct numerical simulation of the Navier-Stokes equations using a spectral method. This agreement provides strong evidence that molecular-level methods for gases can be used to investigate turbulent flows quantitatively.

https://link.aps.org/accepted/10.1103/PhysRevLett.118.064501

Molecular-Level Simulations of Turbulence and Its Decay.

Boundary effects in gravity-driven, dense granular flows down inclined planes are studied using large-scale molecular dynamics simulations. We find that the flow behavior and structure of the flowing pile changes dramatically as we vary the roughness of the supporting base. For a rough, bumpy base, there are three principal flow regimes that depend on the inclination angle θ: at small angles θ θmax, where θmax is the maximum angle for which stable, steady state flow exists, the flow is unstable; and for θr<θ<θmax, the energy input from gravity is balanced by that dissipated through friction and the system reaches a stable, steady state flow. In the stable regime, we find no slip boundary conditions with a bulk density that is independent of the height above the base. For a chute base that is ordered, the steady state regime splits into a further three distinct flow regimes: at lower angles, the flowing system self-organizes ...

Boundary effects and self-organization in dense granular flows

Parallel computing offers new capabilities for using molecular dynamics (MD) to simulate larger numbers of atoms and longer time scales. In this paper we discuss two methods we have used to implement the embedded atom method (EAM) formalism for molecular dynamics on multiple-instruction/multiple-data (MIMD) parallel computers. The first method (atom-decomposition) is simple and suitable for small numbers of atoms. The second method (force-decomposition) is new and is particularly appropriate for the EAM because all the computations are between pairs of atoms. Both methods have the advantage of not requiring any geometric information about the physical domain being simulated. We present timing results for the two parallel methods on a benchmark EAM problem and briefly indicate how the methods can be used in other kinds of materials MD simulations.

Parallel Molecular Dynamics with the Embedded Atom Method

Discrete element simulations of stress distributions in silos: crossover from two to three dimensions

Multiscale simulation is a promising approach for addressing a variety of real-world engineering problems. Various mathematical approaches have been proposed to link single-scale models of physics into multiscale models. In order to be effective, new multiscale simulation algorithms must be implemented which use partial results provided by single-scale software. This work considers aspects of software design for interfacing to existing single-scale simulation code to perform multiscale simulations on a parallel machine. As a practical example, we extended the large-scale atomistic/molecular massively parallel simulator (LAMMPS) atomistic simulation software to facilitate its efficient use as a component of parallel multiscale-simulation software. This required new library interface functions to LAMMPS that side-stepped its dependence on files for input and output and provided efficient access to LAMMPS’s internal state. As a result, we were able to take advantage of LAMMPS’s single-scale performance without adding any multiscale-specific code to LAMMPS itself. We illustrate the use of LAMMPS as a component in three different modes: as a stand-alone application called by a multiscale code, as a parallel library invoked by a serial multiscale code, and as a parallel library invoked by a parallel multiscale code. We conclude that it is possible to efficiently re-use existing single-scale simulation software as a component in multiscale-simulation software.

Steven J. Plimpton

Papers

Molecular-Level Simulations of Turbulence and Its Decay.

Boundary effects and self-organization in dense granular flows

Parallel Molecular Dynamics with the Embedded Atom Method

Discrete element simulations of stress distributions in silos: crossover from two to three dimensions

Software components for parallel multiscale simulation: an example with LAMMPS