Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant
Carl Caleman,Paul J. van Maaren,Minyan Hong,Jochen S. Hub,Luciano T. Costa,David van der Spoel +5 more
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TLDR
A benchmark for force fields is devised in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant.Abstract:
The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on expe...read more
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GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
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TL;DR: A review of the experimental and computational advances over the past decade in understanding the role of water in the dynamics, structure, and function of proteins focuses on the combination of X-ray and neutron crystallography, NMR, terahertz spectroscopy, mass spectroscopic, thermodynamics, and computer simulations to reveal how water assist proteins in their function.
References
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Molecular dynamics with coupling to an external bath.
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Michael P. Allen,D. J. Tildesley +1 more
TL;DR: In this paper, the gear predictor -corrector is used to calculate forces and torques in a non-equilibrium molecular dynamics simulation using Monte Carlo methods. But it is not suitable for the gear prediction problem.
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
TL;DR: PfPMP1)与感染红细胞、树突状组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�ly.