Version 9 of the Amber simulation programs includes a new semi-empirical hybrid QM/MM functionality. This includes support for implicit solvent (generalized Born) and for periodic explicit solvent simulations using a newly developed QM/MM implementation of the particle mesh Ewald (PME) method. The code provides sufficiently accurate gradients to run constant energy QM/MM MD simulations for many...

We present a new hybrid explicit/implicit solvent method for dynamics simulations of macromolecular systems. The method models explicitly the hydration of the solute by either a layer or sphere of water molecules, and the generalized Born (GB) theory is used to treat the bulk continuum solvent outside the explicit simulation volume. To reduce the computational cost, we implemented a multigrid m...

The microsolvation of the suberate dianion, -O2C(CH2)6CO2-, with two separate charge centers was studied by photoelectron spectroscopy and molecular dynamics simulation one solvent molecule at a time for up to 20 waters. It is shown that the two negative charges are solvated in the linear suberate alternately. As the solvent number increases, the negative charges are screened and a conformation...

In the absence of solvent composite machine, because the radius of drum winding and rewinding roller in the transmission process is changing. With the coiled material rolls diameter more and more large, and put the curly size getting smaller and smaller, this has the certain difficulty for the tension control. Therefore, good tension control is non solvent composite is very important. Analyzed ...

The proper matching of force field and solvent is critical to obtain correct result in molecular dynamics simulation of bio-molecules. This problem has been intensively investigated for protein but not for RNA yet. In this paper, we use standard molecular dynamics and replica exchange molecular dynamics to take a series of tests on the RNA stability under different combinations of Amber force f...

Molecular dynamics simulations of supercritical electrolyte solutions with three different ion–water models are performed to study the anion–cation potential of mean force of an infinitely dilute aqueous NaCl solution in the vicinity of the solvent’s critical point. The association constant for the ion pair Na/Cl and the constant of equilibrium between the solvent-separated and the contact ion ...

A method for measuring the pair interaction potential between colloidal particles by extrapolation measurement of collective structure to infinite dilution is presented and explored using simulation and experiment. The method is particularly well suited to systems in which the colloid is fluorescent and refractive index matched with the solvent. The method involves characterizing the potential ...

A pseudo-3D lattice gas-based Monte Carlo simulation is used to reproduce dual-scale non-equilibrium structures formed from drying colloidal nanoparticle solutions. Morphologies possessing multiple length scale features are recreated by coupling the chemical potential to the solvent density, modelling a film thickness-dependent disjoining pressure. By assigning a sigmoidal form to the chemical ...

X-ray crystallography and cryo-electron microscopy are two popular methods for the structure determination of biological molecules. Atomic structures are derived through the fitting and refinement of an initial model into electron density maps constructed by both experiments. Two computational approaches, MDFF and xMDFF, have been developed to facilitate this process by integrating the experime...

Recent studies have shown that explicit solvent molecular dynamics (MD) simulation followed by structural averaging can consistently improve protein structure models. We find that improvement upon averaging is not limited to explicit water MD simulation, as consistent improvements are also observed for more efficient implicit solvent MD or Monte Carlo minimization simulations. To determine the ...