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

A potential model intended to be a general purpose model for the condensed phases of water is presented. TIP4P/2005 is a rigid four site model which consists of three fixed point charges and one Lennard-Jones center. The parametrization has been based on a fit of the temperature of maximum density (indirectly estimated from the melting point of hexagonal ice), the stability of several ice polymorphs and other commonly used target quantities. The calculated properties include a variety of thermodynamic properties of the liquid and solid phases, the phase diagram involving condensed phases, properties at melting and vaporization, dielectric constant, pair distribution function, and self-diffusion coefficient. These properties cover a temperature range from 123to573K and pressures up to 40000bar. The model gives an impressive performance for this variety of properties and thermodynamic conditions. For example, it gives excellent predictions for the densities at 1bar with a maximum density at 278K and an aver...

http://cacharro.quim.ucm.es/publicaciones/JCP_123_234505_2005.pdf

A general purpose model for the condensed phases of water: TIP4P/2005

Changes in portlandite morphology with solvent composition: Atomistic simulations and experiment

where A represents the magnetic vector potential, is an integral of the hydromagnetic equations. This -integral made it possible to formulate a variational principle for the force-free magnetic fields. The integral expresses the fact that motions cannot transform a given field in an entirely arbitrary different field, if the conductivity of the medium isconsidered infinite. In this paper we shall show that the full set of hydromagnetic equations admit five more integrals, besides the energy integral, if dissipative processes are absent. These integrals, as we shall presently verify, are I2 =fbHvdV, (2)

Proceedings of the National Academy of Sciences

The ability of several water models to predict the properties of ices is discussed. The emphasis is put on the results for the densities and the coexistence curves between the different ice forms. It is concluded that none of the most commonly used rigid models is satisfactory. A new model specifically designed to cope with solid-phase properties is proposed. The parameters have been obtained by fitting the equation of state and selected points of the melting lines and of the coexistence lines involving different ice forms. The phase diagram is then calculated for the new potential. The predicted melting temperature of hexagonal ice (Ih) at 1 bar is 272.2 K. This excellent value does not imply a deterioration of the rest of the properties. In fact, the predictions for both the densities and the coexistence curves are better than for TIP4P, which previously yielded the best estimations of the ice properties.

/pdf/a-potential-model-for-the-study-of-ices-and-amorphous-water-2dl9vf4x61.pdf

A potential model for the study of ices and amorphous water: TIP4P/Ice.

Over the last forty years many computer simulations of water have been performed using rigid non-polarizable models. Since these models describe water interactions in an approximate way it is evident that they cannot reproduce all of the properties of water. By now many properties for these kinds of models have been determined and it seems useful to compile some of these results and provide a critical view of the successes and failures. In this paper a test is proposed in which 17 properties of water, from the vapour and liquid to the solid phases, are taken into account to evaluate the performance of a water model. A certain number of points between zero (bad agreement) and ten (good agreement) are given for the predictions of each model and property. We applied the test to five rigid non-polarizable models, TIP3P, TIP5P, TIP4P, SPC/E and TIP4P/2005, obtaining an average score of 2.7, 3.7, 4.7, 5.1, and 7.2 respectively. Thus although no model reproduces all properties, some models perform better than others. It is clear that there are limitations for rigid non-polarizable models. Neglecting polarizability prevents an accurate description of virial coefficients, vapour pressures, critical pressure and dielectric constant. Neglecting nuclear quantum effects prevents an accurate description of the structure, the properties of water below 120 K and the heat capacity. It is likely that for rigid non-polarizable models it may not be possible to increase the score in the test proposed here beyond 7.6. To get closer to experiment, incorporating polarization and nuclear quantum effects is absolutely required even though a substantial increase in computer time should be expected. The test proposed here, being quantitative and selecting properties from all phases of water can be useful in the future to identify progress in the modelling of water.

/pdf/simulating-water-with-rigid-non-polarizable-models-a-general-4316yz77p3.pdf

Simulating water with rigid non-polarizable models: a general perspective

The performance of several popular water models (TIP3P, TIP4P, TIP5P and TIP4P/2005) is analyzed. For that purpose the predictions for ten different properties of water are investigated, namely: 1. vapour–liquid equilibria (VLE) and critical temperature; 2. surface tension; 3. densities of the different solid structures of water (ices); 4. phase diagram; 5. melting-point properties; 6. maximum in the density of water at room pressure and thermal coefficients α and κT; 7. structure of liquid water and ice; 8. equation of state at high pressures; 9. self-diffusion coefficient; 10. dielectric constant. For each property, the performance of each model is analyzed in detail with a critical discussion of the possible reason of the success or failure of the model. A final judgement on the quality of these models is provided. TIP4P/2005 provides the best description of almost all properties of the list, the only exception being the dielectric constant. In second position, TIP5P and TIP4P yield a similar performance overall, and the last place with the poorest description of the water properties is provided by TIP3P. The ideas leading to the proposal and design of the TIP4P/2005 are also discussed in detail. TIP4P/2005 is probably close to the best description of water that can be achieved with a non-polarizable model described by a single Lennard-Jones (LJ) site and three charges.

What ice can teach us about water interactions: a critical comparison of the performance of different water models.

In this work we present an implementation for the calculation of the melting point of ice Ih from direct coexistence of the solid-liquid interface. We use molecular dynamics simulations of boxes containing liquid water and ice in contact. The implementation is based on the analysis of the evolution of the total energy along NpT simulations at different temperatures. We report the calculation of the melting point of ice Ih at 1 bar for seven water models: SPC/E, TIP4P, TIP4P-Ew, TIP4P/ice, TIP4P/2005, TIP5P, and TIP5P-E. The results for the melting temperature from the direct coexistence simulations of this work are in agreement within the statistical uncertainty with those obtained previously by us from free energy calculations. By taking into account the results of this work and those of our free energy calculations, recommended values of the melting point of ice Ih at 1 bar for the above mentioned water models are provided. © 2006 American Institute of Physics. DOI: 10.1063/1.2183308

http://catalan.quim.ucm.es/pdf/cvegapaper106.pdf

José L. F. Abascal

Papers

A general purpose model for the condensed phases of water: TIP4P/2005

A potential model for the study of ices and amorphous water: TIP4P/Ice.

Simulating water with rigid non-polarizable models: a general perspective

What ice can teach us about water interactions: a critical comparison of the performance of different water models.

The melting point of ice Ih for common water models calculated from direct coexistence of the solid-liquid interface.