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

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecu- lar simulation program. It has been developed over the last three decades with a primary focus on molecules of bio- logical interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estima- tors, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numer- ous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.

/pdf/charmm-the-biomolecular-simulation-program-4kexem0xkx.pdf

CHARMM: the biomolecular simulation program.

Although molecular dynamics (MD) simulations of biomolecular systems often run for days to months, many events of great scientific interest and pharmaceutical relevance occur on long time scales that remain beyond reach. We present several new algorithms and implementation techniques that significantly accelerate parallel MD simulations compared with current stateof- the-art codes. These include a novel parallel decomposition method and message-passing techniques that reduce communication requirements, as well as novel communication primitives that further reduce communication time. We have also developed numerical techniques that maintain high accuracy while using single precision computation in order to exploit processor-level vector instructions. These methods are embodied in a newly developed MD code called Desmond that achieves unprecedented simulation throughput and parallel scalability on commodity clusters. Our results suggest that Desmond?s parallel performance substantially surpasses that of any previously described code. For example, on a standard benchmark, Desmond?s performance on a conventional Opteron cluster with 2K processors slightly exceeded the reported performance of IBM?s Blue Gene/L machine with 32K processors running its Blue Matter MD code.

/pdf/scalable-algorithms-for-molecular-dynamics-simulations-on-4x8mdh8p24.pdf

Scalable algorithms for molecular dynamics simulations on commodity clusters

When Szent-Gyorgyi called water the “matrix of life”,1 he was echoing an old sentiment. Paracelsus in the 16th century said that “water was the matrix of the world and of all its creatures.”2 But Paracelsus’s notion of a matrixsan active substance imbued with fecund, life-giving propertiess was quite different from the picture that, until very recently, molecular biologists have tended to hold of water’s role in the chemistry of life. Although acknowledging that liquid water has some unusual and important physical and chemical propertiessits potency as a solvent, its ability to form hydrogen bonds, its amphoteric naturesbiologists have regarded it essentially as the backdrop on which life’s molecular components are arrayed. It used to be common practice, for example, to perform computer simulations of biomolecules in a vacuum. Partly this was because the computational intensity of simulating a polypeptide chain was challenging even without accounting for solvent molecules too, but it also reflected the prevailing notion that water does little more than temper or moderate the basic physicochemical interactions responsible for molecular biology. What Gerstein and Levitt said 9 years ago remains true today: “When scientists publish models of biological molecules in journals, they usually draw their models in bright colors and place them against a plain, black background”.3 Curiously, this neglect of water as an active component of the cell went hand in hand with the assumption that life could not exist without it. That was basically an empirical conclusion derived from our experience of life on Earth: environments without liquid water cannot sustain life, and special strategies are needed to cope with situations in which, because of extremes of either heat or cold, the liquid is scarce.4-6 The recent confirmation that there is at least one world rich in organic molecules on which rivers and perhaps shallow seas or bogs are filled with nonaqueous fluidsthe liquid hydrocarbons of Titan7smight now bring some focus, even urgency, to the question of whether water is indeed a * E-mail: p.ball@nature.com. Philip Ball is a science writer and a consultant editor for Nature, where he worked as an editor for physical sciences for more than 10 years. He holds a Ph.D. in physics from the University of Bristol, where he worked on the statistical mechanics of phase transitions in the liquid state. His book H2O: A Biography of Water (Weidenfeld & Nicolson, 1999) was a survey of the current state of knowledge about the behavior of water in situations ranging from planetary geomorphology to cell biology. He frequently writes about aspects of water science for both the popular and the technical media.

https://www.philipball.co.uk/images/stories/docs/pdf/ChemRev_final.pdf

Water as an Active Constituent in Cell Biology

Water droplets on rugged hydrophobic surfaces typically exhibit one of the following two states: (i) the Wenzel state [Wenzel RN (1936) Ind Eng Chem 28:988–994] in which water droplets are in full contact with the rugged surface (referred as the wetted contact) or (ii) the Cassie state [Cassie, ABD, Baxter S (1944) Trans Faraday Soc 40:546–551] in which water droplets are in contact with peaks of the rugged surface as well as the “air pockets” trapped between surface grooves (the composite contact). Here, we show large-scale molecular dynamics simulation of transition between Wenzel state and Cassie state of water droplets on a periodic nanopillared hydrophobic surface. Physical conditions that can strongly affect the transition include the height of nanopillars, the spacing between pillars, the intrinsic contact angle, and the impinging velocity of water nanodroplet (“raining” simulation). There exists a critical pillar height beyond which water droplets on the pillared surface can be either in the Wenzel state or in the Cassie state, depending on their initial location. The free-energy barrier separating the Wenzel and Cassie state was computed on the basis of a statistical-mechanics method and kinetic raining simulation. The barrier ranges from a few tenths of kBT0 (where kB is the Boltzmann constant, and T0 is the ambient temperature) for a rugged surface at the critical pillar height to ≈8 kBT0 for the surface with pillar height greater than the length scale of water droplets. For a highly rugged surface, the barrier from the Wenzel-to-Cassie state is much higher than from Cassie-to-Wenzel state. Hence, once a droplet is trapped deeply inside the grooves, it would be much harder to relocate on top of high pillars.

/pdf/coexistence-and-transition-between-cassie-and-wenzel-state-1fxegyjm77.pdf

Coexistence and transition between Cassie and Wenzel state on pillared hydrophobic surface

Molecular dynamics computer simulation was carried out to investigate the dynamics of vapor phase homogeneous nucleation at the triple point temperature under supersaturation ratio 6.8 for a Lennard-Jones fluid. To control the system temperature, the 5000 target particles were mixed with 5000 soft-core carrier gas particles. The observed nucleation rate is seven orders of magnitude larger than prediction of a classical nucleation theory. The kinetically defined critical nucleus size, at which the growth and decay rates are balanced, is 30–40, as large as the thermodynamically defined value of 25.4 estimated with the classical theory. From the cluster size distribution in the steady state region, the free energy of cluster formation is estimated, which diminishes the difference between the theoretical prediction and the simulational result concerning the nucleation rate.

http://web.mst.edu/~hale/argonMC/References/JCP.1998.Yasuoka.MD.LJ.nucl.pdf

Molecular dynamics of homogeneous nucleation in the vapor phase. I. Lennard-Jones fluid

Position and orientation of water protons need to be specified when the molecular simulation studies are performed for clathrate hydrates. Positions of oxygen atoms in water are experimentally determined by X-ray diffraction analysis of clathrate hydrate structures, but positions of water hydrogen atoms in the lattice are disordered. This study reports a determination of the water proton coordinates in unit cell of structure I (sI), II (sII), and H (sH) clathrate hydrates that satisfy the ice rules, have the lowest potential energy configuration for the protons, and give a net zero dipole moment. Possible proton coordinates in the unit cell were chosen by analyzing the symmetry of protons on the hexagonal or pentagonal faces in the hydrate cages and generating all possible proton distributions which satisfy the ice rules. We found that in the sI and sII unit cells, proton distributions with small net dipole moments have fairly narrow potential energy spreads of about 1 kJ/mol. The total Coulomb potential on a test unit charge placed in the cage center for the minimum energy/minimum dipole unit cell configurations was calculated. In the sI small cages, the Coulomb potential energy spread in each class of cage is less than 0.1 kJ/mol, while the potential energy spread increases to values up to 6 kJ/mol in sH and 15 kJ/mol in the sII cages. The guest environments inside the cages can therefore be substantially different in the sII case. Cartesian coordinates for oxygen and hydrogen atoms in the sI, sII, and sH unit cells are reported for reference.

/pdf/water-proton-configurations-in-structures-i-ii-and-h-mok6z5ej82.pdf

Water proton configurations in structures I, II, and H clathrate hydrate unit cells.

This paper describes an experimental study on the statistical nature of clathrate-hydrate nucleation in a quiescent hydrochlorofluorocarbon-in-water system in which a hydrate was once formed and th...

Statistical study of clathrate-hydrate nucleation in a water/hydrochlorofluorocarbon system: Search for the nature of the memory effect

Homogeneous nucleation process in the vapor phase of water is investigated with a molecular dynamics computer simulation at 350 K under supersaturation ratio 7.3. Using a method similar to Lennard-Jones fluid (Part I), the nucleation rate is three orders of magnitude smaller than prediction of a classical nucleation theory. The kinetically defined critical nucleus size is 30–45, much larger than the thermodynamically defined value of 1.0 estimated with the classical theory. Free energy of cluster formation is estimated from the cluster size distribution in steady state time region. The predicted nucleation rate with this free energy agrees with the simulation result. It is concluded that considering the cluster size dependence of surface tension is very important.

/pdf/molecular-dynamics-of-homogeneous-nucleation-in-the-vapor-4v9n9u8itt.pdf

Kenji Yasuoka

Papers

Coexistence and transition between Cassie and Wenzel state on pillared hydrophobic surface

Molecular dynamics of homogeneous nucleation in the vapor phase. I. Lennard-Jones fluid

Water proton configurations in structures I, II, and H clathrate hydrate unit cells.

Statistical study of clathrate-hydrate nucleation in a water/hydrochlorofluorocarbon system: Search for the nature of the memory effect

Molecular dynamics of homogeneous nucleation in the vapor phase. II. Water