Journal ArticleDOI
Calibration and Testing of a Water Model for Simulation of the Molecular Dynamics of Proteins and Nucleic Acids in Solution
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TLDR
In this paper, a flexible three-centered water model (F3C) is proposed for simulation of biological macromolecules in solution, and the model is further tested by comparing calculated energetic, structural, and dynamic properties of liquid water, at several temperatures and pressures, with experiment.Abstract:
The objective of this work is to obtain a water model for simulations of biological macromolecules in solution. A pragmatic approach is taken in which we use the same type of force field for the water as used for the solute and derive the water potential as an integral part of the ENCAD macromolecular potential.1,2 Here we describe a flexible three-centered water model (F3C), which has already been used for many large-scale biological simulations, and compare it with other water models. The model is further tested by comparing calculated energetic, structural, and dynamic properties of liquid water, at several temperatures and pressures, with experiment. The F3C model is extremely simple and fits experimental data well for different temperatures, pressures, system sizes, and integration time steps. Because the F3C model works well with short-range truncation, it is well-suited to high-speed computation of long molecular dynamics trajectories of macromolecules in solution.read more
Citations
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Journal ArticleDOI
Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K
Pekka Mark and,Lennart Nilsson +1 more
TL;DR: In this paper, the effects of velocity rescaling on the self-diffusion coefficient D and radial distribution functions, gOO, gOH, and gHH for all five water models were determined and compared to experimental data.
Book ChapterDOI
Force fields for protein simulations
Jay W. Ponder,David A. Case +1 more
TL;DR: The chapter focuses on a general description of the force fields that are most commonly used at present and gives an indication of the directions of current research that may yield better functions in the near future.
Journal ArticleDOI
Empirical force fields for biological macromolecules: overview and issues.
TL;DR: An overview of the issues associated with the development and application of empirical force fields to biomolecular systems and a summary of the force fields commonly applied to the different classes of biomolecules are presented.
Journal ArticleDOI
On the Water−Carbon Interaction for Use in Molecular Dynamics Simulations of Graphite and Carbon Nanotubes
TL;DR: In this paper, a linear relationship between the contact angle and the water monomer binding energy on graphite was established and a new route to calibrate interaction potential parameters was presented, which was obtained by applying a carbon−oxygen Lennard-Jones potential with parameters eCO = 0.392 kJ mol-1 and σCO = 3.19 A.
Journal ArticleDOI
Flexible simple point-charge water model with improved liquid-state properties
TL;DR: A new flexible simple point-charge water model was derived by optimizing bulk diffusion and dielectric constants to the experimental values via the equilibrium bond length and angle and extensive comparisons of thermodynamic, structural, and kinetic properties indicate that the new model is much improved over the standard SPC model and its overall performance is comparable to or even better than the extended SPC models.
References
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Journal ArticleDOI
Comparison of simple potential functions for simulating liquid water
TL;DR: In this article, the authors compared the Bernal Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P potential functions for liquid water in the NPT ensemble at 25°C and 1 atm.
Book
Computer Simulation of Liquids
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.
Journal ArticleDOI
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Bernard R. Brooks,Robert E. Bruccoleri,Barry D. Olafson,David J. States,S. Swaminathan,Martin Karplus +5 more
TL;DR: The CHARMM (Chemistry at Harvard Macromolecular Mechanics) as discussed by the authors is a computer program that uses empirical energy functions to model macromolescular systems, and it can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations.
Journal ArticleDOI
The missing term in effective pair potentials
TL;DR: On the other hand, in this paper, a superparamagnetically collapsed Mossbauer spectrum is obtained for carbon with fewer active sites, and these particles sinter and carburize in a manner more similar to that of Fe particles supported on graphite.
Book ChapterDOI
Interaction Models for Water in Relation to Protein Hydration
TL;DR: In this article, a three-point charge model (on hydrogen and oxygen positions) with a Lennard-Jones 6-12 potential on the oxygen positions only was developed, and parameters for the model were determined from 12 molecular dynamics runs covering the two-dimensional parameter space of charge and oxygen repulsion.