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

Analog resistive memories promise to reduce the energy of neural networks by orders of magnitude. However, the write variability and write nonlinearity of current devices prevent neural networks from training to high accuracy. We present a novel periodic carry method that uses a positional number system to overcome this while maintaining the benefit of parallel analog matrix operations. We demonstrate how noisy, nonlinear TaO x devices that could only train to 80% accuracy on MNIST, can now reach 97% accuracy, only 1% away from an ideal numeric accuracy of 98%. On a file type dataset, the TaO x devices achieve ideal numeric accuracy. In addition, low noise, linear Li 1−x CoO 2 devices train to ideal numeric accuracies using periodic carry on both datasets.

Achieving ideal accuracies in analog neuromorphic computing using periodic carry

Icarus is a 2D Direct Simulation Monte Carlo (DSMC) code which has been optimized for the parallel computing environment. The code is based on the DSMC method of Bird[11.1] and models from free-molecular to continuum flowfields in either cartesian (x, y) or axisymmetric (z, r) coordinates. Computational particles, representing a given number of molecules or atoms, are tracked as they have collisions with other particles or surfaces. Multiple species, internal energy modes (rotation and vibration), chemistry, and ion transport are modeled. A new trace species methodology for collisions and chemistry is used to obtain statistics for small species concentrations. Gas phase chemistry is modeled using steric factors derived from Arrhenius reaction rates or in a manner similar to continuum modeling. Surface chemistry is modeled with surface reaction probabilities; an optional site density, energy dependent, coverage model is included. Electrons are modeled by either a local charge neutrality assumption or as discrete simulational particles. Ion chemistry is modeled with electron impact chemistry rates and charge exchange reactions. Coulomb collision cross-sections are used instead of Variable Hard Sphere values for ion-ion interactions. The electro-static fields can either be: externally input, a Langmuir-Tonks model or from a Green's Function (Boundary Element) based Poison Solver. Icarus has been used for subsonic to hypersonic, chemically reacting, and plasma flows. The Icarus software package includes the grid generation, parallel processor decomposition, post-processing, and restart software. The commercial graphics package, Tecplot, is used for graphics display. All of the software packages are written in standard Fortran.

/pdf/icarus-a-2-d-direct-simulation-monte-carlo-dsmc-code-for-3pil222e4o.pdf

Icarus: A 2-D Direct Simulation Monte Carlo (DSMC) Code for Multi-Processor Computers

Optimizing legacy molecular dynamics software with directive-based offload

Multiparticle collision dynamics (MPCD) is a particle-based fluid simulation technique that is becoming increasingly popular for mesoscale fluid modeling. However, some confusion and conflicting results persist in literature regarding several important methodological details, in particular the enforcement of the no-slip condition and thermostatting in forced flow. These issues persist in simple flows past stationary boundaries, which we exclusively focus on here. We discuss the parametrization of MPCD fluids and its consequences for fluid-solid boundaries in great detail, and show that the method of virtual particles proposed by Lamura et al. and adopted by many others is required only for parameter choices that lead to viscosities dominated by collisional contributions. We test several implementations of the virtual particle method and discuss how to completely eliminate slip at stationary boundaries. We also show that stochastic boundary reflection rules are inherently problematic for forced flow and suggest a possible remedy. Finally, we discuss the most robust way to achieve forced flow and evaluate several thermostatting methods in the process. All discussion is limited to solid objects that do not move as a result of collisions with MPCD particles (i.e., walls). However, the results can be extended to solutes that experience forces and torques due to interactions with MPCD particles (e.g., colloids). The detailed analysis presented for this simple case provides the level of rigor and accuracy to the MPCD method required for the study of more complex systems.

No-slip boundary conditions and forced flow in multiparticle collision dynamics.

Peridynamics is a nonlocal extension of classical continuum mechanics. The discrete peridynamic model has the same computational structure as a molecular dynamics model. This document provides a brief overview of the peridynamic model of a continuum, then discusses how the peridynamic model is discretized within LAMMPS. An example problem is also included.

Steven J. Plimpton

Papers

Achieving ideal accuracies in analog neuromorphic computing using periodic carry

Icarus: A 2-D Direct Simulation Monte Carlo (DSMC) Code for Multi-Processor Computers

Optimizing legacy molecular dynamics software with directive-based offload

No-slip boundary conditions and forced flow in multiparticle collision dynamics.

Peridynamics with LAMMPS: A User Guide v0.3 Beta