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.

Fast parallel algorithms for short-range molecular dynamics

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

Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions Not only does this combination of a

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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation

Microstructures and properties of high-entropy alloys

By removing the fastest degrees of freedom, constraints allow for an increase of the time step in molecular simulations. In the last decade parallel simulations have become commonplace. However, up till now efficient parallel constraint algorithms have not been used with domain decomposition. In this paper the parallel linear constraint solver (P-LINCS) is presented, which allows the constraining of all bonds in macromolecules. Additionally the energy conservation properties of (P-)LINCS are assessed in view of improvements in the accuracy of uncoupled angle constraints and integration in single precision.

P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation

We report on large-scale nonequilibrium molecular dynamics simulations of shock wave compression in tantalum single crystals. Two new embedded atom method interatomic potentials of Ta have been developed and optimized by fitting to experimental and density functional theory data. The potentials reproduce the isothermal equation of state of Ta up to 300 GPa. We examined the nature of the plastic deformation and elastic limits as functions of crystal orientation. Shock waves along (100), (110), and (111) exhibit elastic-plastic two-wave structures. Plastic deformation in shock compression along (110) is due primarily to the formation of twins that nucleate at the shock front. The strain-rate dependence of the flow stress is found to be orientation dependent, with (110) shocks exhibiting the weaker dependence. Premelting at a temperature much below that of thermodynamic melting at the shock front is observed in all three directions for shock pressures above about 180 GPa.

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Shock-induced plasticity in tantalum single crystals: Interatomic potentials and large-scale molecular-dynamics simulations

We report on recent molecular-dynamics (MD) fracture simulations of mode-I tensile loading at high strain rates. Because cracks emit sound waves, previous simulations became unreliable beyond one sound traversal time. Using massively parallel MD, we show how to eliminate unwanted boundary effects and study unimpeded crack propagation mechanisms. In order to represent tensile stress conditions near the crack tip, we employ uniaxial, homogeneously expanding periodic boundary conditions, examining the effects of strain rate, temperature, and interaction potential. Because our samples are sufficiently large, we see dislocations being emitted from the crack tip at nearly the shear-wave sound speed ${\mathit{c}}_{\mathit{s}}$. As they move many lattice spacings away from the crack, they slow down, finally moving at about 2/3${\mathit{c}}_{\mathit{s}}$. Each time dislocations are emitted, the crack tip ``fishtails,'' and at sufficiently high strain, the crack can fork; dislocations can climb and become nucleation sites for additional microcracks. We find that we can suppress ductile behavior by including viscous damping in the equations of motion, thereby demonstrating a transition to brittle crack propagation as static, zero-strain-rate conditions are approached. Finally, we show that, by altering only the attractive tail of the pair potential, we can change a ductile material into a brittle one. Under dynamic crack propagation, the distinction between ductile and brittle behavior is blurred: in brittle materials, dislocations are asymptotically bound to the crack tip, while in ductile materials, they can escape.

Fracture simulations using large-scale molecular dynamics

We use multimillion-atom molecular dynamics simulations to study shock wave propagation in fcc crystals As shown recently, shock waves along the direction form intersecting stacking faults by slippage along {l_brace}111{r_brace} close-packed planes at sufficiently high shock strengths We find even more interesting behavior of shocks propagating in other low-index directions: for the case, an elastic precursor separates the shock front from the slipped (plastic) region Shock waves along the direction generate a leading solitary wave train, followed (at sufficiently high shock speeds) by an elastic precursor, and then a region of complex plastic deformation (c) 2000 The American Physical Society

Orientation dependence in molecular dynamics simulations of shocked single crystals

The thermodynamic properties of various phases of tin are calculated employing the method of adiabatic switching with modified embedded atom method (MEAM) potentials. The experimental $\ensuremath{\alpha}\ensuremath{\rightarrow}\ensuremath{\beta}$ and $\ensuremath{\beta}\ensuremath{\rightarrow}\mathrm{liquid}$ transition temperatures are reproduced within an 11% accuracy. Good agreement with experiments is also obtained for other thermodynamic quantities. We demonstrate the versatility and accuracy of MEAM by how well it reproduces both metallic and covalent phases of tin over a wide temperature range and over a wide range of densities.

Equilibrium and Thermodynamic Properties of Grey, White, and Liquid Tin

The Nos\'e-Hoover thermostat, which is often used in the hope of modifying molecular dynamics trajectories in order to achieve canonical-ensemble averages, has hidden in it a Toda ``demon,'' which can give rise to unwanted, noncanonical undulations in the instantaneous kinetic temperature We show how these long-lived oscillations arise from insufficient coupling of the thermostat to the atoms, and give straightforward, practical procedures for avoiding this weak-coupling pathology in isothermal molecular dynamics simulations

Ramon Ravelo

Papers

Shock-induced plasticity in tantalum single crystals: Interatomic potentials and large-scale molecular-dynamics simulations

Fracture simulations using large-scale molecular dynamics

Orientation dependence in molecular dynamics simulations of shocked single crystals

Equilibrium and Thermodynamic Properties of Grey, White, and Liquid Tin

Thermostatted molecular dynamics: How to avoid the Toda demon hidden in Nosé-Hoover dynamics.