Introduction Statistical mechanics Molecular dynamics Monte Carlo methods Some tricks of the trade How to analyse the results Advanced simulation techniques Non-equilibrium molecular dynamics Brownian dynamics Quantum simulations Some applications Appendix A: Computers and computer simulation Appendix B: Reduced units Appendix C: Calculation of forces and torques Appendix D: Fourier transforms Appendix E: The gear predictor - corrector Appendix F: Programs on microfiche Appendix G: Random numbers References Index.

Computer Simulation of Liquids

The AMBER lipid force field has been updated to create Lipid14, allowing tensionless simulation of a number of lipid types with the AMBER MD package. The modular nature of this force field allows numerous combinations of head and tail groups to create different lipid types, enabling the easy insertion of new lipid species. The Lennard-Jones and torsion parameters of both the head and tail groups have been revised and updated partial charges calculated. The force field has been validated by simulating bilayers of six different lipid types for a total of 0.5 μs each without applying a surface tension; with favorable comparison to experiment for properties such as area per lipid, volume per lipid, bilayer thickness, NMR order parameters, scattering data, and lipid lateral diffusion. As the derivation of this force field is consistent with the AMBER development philosophy, Lipid14 is compatible with the AMBER protein, nucleic acid, carbohydrate, and small molecule force fields.

/pdf/lipid14-the-amber-lipid-force-field-1gj0t3c4bx.pdf

Lipid14: The Amber Lipid Force Field

Some frequently encountered deficiencies in all-atom molecular simulations, such as nonspecific protein–protein interactions being too strong, and unfolded or disordered states being too collapsed, suggest that proteins are insufficiently well solvated in simulations using current state-of-the-art force fields. To address these issues, we make the simplest possible change, by modifying the short-range protein–water pair interactions, and leaving all the water–water and protein–protein parameters unchanged. We find that a modest strengthening of protein–water interactions is sufficient to recover the correct dimensions of intrinsically disordered or unfolded proteins, as determined by direct comparison with small-angle X-ray scattering (SAXS) and Forster resonance energy transfer (FRET) data. The modification also results in more realistic protein-protein affinities, and average solvation free energies of model compounds which are more consistent with experiment. Most importantly, we show that this scaling...

https://pubs.acs.org/doi/pdf/10.1021/ct500569b

Balanced Protein–Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association

The weighted ensemble (WE) methodology orchestrates quasi-independent parallel simulations run with intermittent communication that can enhance sampling of rare events such as protein conformational changes, folding, and binding. The WE strategy can achieve superlinear scaling—the unbiased estimation of key observables such as rate constants and equilibrium state populations to greater precision than would be possible with ordinary parallel simulation. WE software can be used to control any dynamics engine, such as standard molecular dynamics and cell-modeling packages. This article reviews the theoretical basis of WE and goes on to describe successful applications to a number of complex biological processes—protein conformational transitions, (un)binding, and assembly processes, as well as cell-scale processes in systems biology. We furthermore discuss the challenges that need to be overcome in the next phase of WE methodological development. Overall, the combined advances in WE methodology and software ...

/pdf/weighted-ensemble-simulation-review-of-methodology-58toey9mvq.pdf

Weighted Ensemble Simulation: Review of Methodology, Applications, and Software

1Department of Chemical and Biomolecular Engineering, The University of Notre Dame; 2Thermodynamics Research Center, National Institute of Standards and Technology; 3Chemical Engineering Department, Brigham Young University; 4Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health; 5Department of Chemical and Biomolecular Engineering, The University of Akron

/pdf/best-practices-for-computing-transport-properties-1-self-4pg26l3j2o.pdf

Best Practices for Computing Transport Properties 1. Self-Diffusivity and Viscosity from Equilibrium Molecular Dynamics [Article v1.0]

Temperature control algorithms in molecular dynamics (MD) simulations are necessary to study isothermal systems. However, these thermostatting algorithms alter the velocities of the particles and thus modify the dynamics of the system with respect to the microcanonical ensemble, which could potentially lead to thermostat-dependent dynamical artifacts. In this study, we investigate how six well-established thermostat algorithms applied with different coupling strengths and to different degrees of freedom affect the dynamics of various molecular systems. We consider dynamic processes occurring on different times scales by measuring translational and rotational self-diffusion as well as the shear viscosity of water, diffusion of a small molecule solvated in water, and diffusion and the dynamic structure factor of a polymer chain in water. All of these properties are significantly dampened by thermostat algorithms which randomize particle velocities, such as the Andersen thermostat and Langevin dynamics, when...

Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations

A multiscale model is presented to elucidate protein adsorption and transport behaviors in ion-exchange chromatography (IEC) adsorbent particles that have either an open pore structure or charged dextran polymers grafted into the pores. Molecular dynamics simulation is used to determine protein diffusion and partitioning in different regions of the adsorbent pore, and these outputs are used in numerical simulations of mass transfer to determine the intraparticle protein concentration profile and the mass-transfer rate. Modeling results indicate that, consistent with experimental observations, protein transport can be faster in the polymer-grafted material compared to the open pore case. This occurs when favorable partitioning of protein into the polymer-filled pore space is combined with relatively high protein mobility within this region. The modeling approach presented here should be applicable to proteins and adsorbents with different properties, and could help elucidate the factors that control adsorption and transport in various IEC systems. © 2014 American Institute of Chemical Engineers AIChE J, 60: 3888–3901, 2014

Multiscale modeling of protein adsorption and transport in macroporous and polymer-grafted ion exchangers

Multiscale simulation is used to study the adsorption of lysozyme onto ion exchangers obtained by grafting charged polymers into a porous matrix, in systems with various polymer properties and strengths of electrostatic interaction. Molecular dynamics simulations show that protein partitioning into the polymer-filled pore space increases with the overall charge content of the polymers, while the diffusivity in the pore space decreases. However, the combination of greatly increased partitioning and modestly decreased diffusion results in macroscopic transport rates that increase as a function of charge content, as the large concentration driving force due to enhanced pore space partitioning outweighs the reduction in the pore space diffusivity. Matrices having greater charge associated with the grafted polymers also exhibit more diffuse intraparticle concentration profiles during transient adsorption. In systems with a high charge content per polymer and a low protein loading, the polymers preferentially partition toward the surface due to favorable interactions with the surface-bound protein. These results demonstrate the potential of multiscale modeling to illuminate qualitative trends between molecular properties and the adsorption equilibria and kinetic properties observable on macroscopic scales.

Effects of polymer graft properties on protein adsorption and transport in ion exchange chromatography: a multiscale modeling study.

We use multiscale modeling to study how the molecular properties of a protein affect its adsorption and transport in ion exchange chromatography matrices with either open pores or charged polymers grafted into the pore structure Coarse-grained molecular dynamics (MD) simulations of lysozyme, bovine serum albumin, and immunoglobulin show that higher protein net charge leads to greater partitioning into the polymer-grafted pore space but slower diffusion there due to favorable electrostatic interactions, while larger size decreases both pore space partitioning and diffusion due to steric effects of the polymers Mass transfer simulations based on the MD results show that the polymer-grafted systems can enhance the adsorption kinetics if pore space partitioning and diffusion are both sufficiently high The simulations illustrate that to achieve fast adsorption kinetics, there is a tradeoff between favorable binding and rapid diffusion which largely depends on the charge and size of the protein © 2017 American Institute of Chemical Engineers AIChE J, 63: 4564–4575, 2017

Effects of protein properties on adsorption and transport in polymer-grafted ion exchangers: A multiscale modeling study

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Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations

Multiscale modeling of protein adsorption and transport in macroporous and polymer-grafted ion exchangers

Effects of polymer graft properties on protein adsorption and transport in ion exchange chromatography: a multiscale modeling study.

Effects of protein properties on adsorption and transport in polymer-grafted ion exchangers: A multiscale modeling study