It is shown that, by optimizing the placement of a solute in a solvent droplet or in a periodic simulation cell, the number of solvent molecules can be reduced without affecting the quality of the simulation. Q 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 812]815, 1997

Received (received date) Revised (revised date) We investigate a new method for simulating polymer-solvent systems which combines a lattice Boltzmann approach for the uid with a continuum molecular dynamics (MD) model for the polymer chain. The two parts are coupled by a friction force which is proportional to the diierence of the monomer velocity and the uid velocity at the monomer's position....

The understanding of the effect of a solvent on proton transfer requires the elucidation of the solvent contribution to the free energy of solvation. Due to the high dimensionality of the configuration space involved in the problem, the solvent effect can only be modeled via computer simulation for a complex polyatomic solute. While simulation of rather large systems have recently become relati...

A dielectric continuum theory for the solvation of a polar molecule in a polar, polarizable solvent is tested using computer simulations of formaldehyde in water. Many classes of experiments, for example those which measure solvent-shifted vertical transition energies or electron transfer rates, require an explicit consideration of the solvent electronic polarization. Due to the computational c...

Solvent effects on polymer dynamics and structure are investigated using a mesoscopic solvent model that accounts for hydrodynamic interactions among the polymer beads. The simulation method combines molecular dynamics of the polymer chain, interacting with the solvent molecules through intermolecular forces, with mesoscopic multiparticle collision dynamics for the solvent molecules. Changes in...

An attempt to generalize the Langevin dynamics simulation method is presented based on the generalized Langevin theory of liquids, in which the dynamics of both solute and solvent is treated by the generalized Langevin equations, but the integration of the equation of motion of solute is made in the manner similar to the ordinary molecular dynamics simulation with discretized time steps along a...

the molecular dynamics (md) simulation method is used to assess structural details for humanprion protein (hereafter prpn) and its asp178 asn mutant (hereafter prpm) which causes fatalfamilial insomnia disease. the results reveal that the flexibility and instability increase in prpmcould be related to specific amino acids exposed to the solvent. solvation free energy of prpm is 20kjmot1nni2 mor...

Molecular dynamics simulations of opposing polymer brushes at varying surface separation distances were performed to develop a method for conducting a static compression of soft matter. As all separation distances were represented by independent simulations, the proper solvent density for every level of compression needed to be determined to acquire realistic data. This was accomplished by main...