Abstract
A new approach to studying localized chemical events in condensed phases is developed. The approach provides a simple and convenient method for reducing the total number of solvent particles explicitly included in simulations of localized processes while decreasing spurious edge effects. Both energy flow across the boundary and density fluctuations in the simulation region are included; this makes it possible to treat nonequilibrium processes, such as thermal gradients and endothermic or exothermic chemical reactions. The essential element of the approach is the introduction of a soft boundary force and a stochastic buffer region. For simple liquids, the boundary force is determined from the solvent equilibrium structure (radial distribution function) and is readily incorporated into conventional molecular dynamics algorithms. The methodology is illustrated by application to liquid argon in spherical and cubical simulation regions; comparison with standard molceular dynamics results show excellent agreement for structural, dynamic, and thermodynamic properties.
Keywords
Molecular dynamicsExothermic reactionBoundary (topology)Spurious relationshipStatistical physicsNon-equilibrium thermodynamicsEndothermic processSimple (philosophy)Boundary value problemMaterials scienceMechanicsPhysicsThermodynamicsChemistryComputer sciencePhysical chemistryComputational chemistryMathematicsMathematical analysis
Affiliated Institutions
Related Publications
Computer ‘‘experiment’’ for nonlinear thermodynamics of Couette flow
Nonequilibrium computer simulations reveal that the equation of state of fluids undergoing shear flow, varies with strain rate. This observation prompted the development of a no...
A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations
Abstract Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third‐generation point...
CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model
Abstract A fluctuating charge (FQ) force field is applied to molecular dynamics simulations for six small proteins in explicit polarizable solvent represented by the TIP4P‐FQ po...
Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions
This article defines the parameterization and performance of MMFF94 for intermolecular interactions. It specifies the novel “buffered” functional forms used for treating van der...
Are Current Semiempirical Methods Better Than Force Fields? A Study from the Thermodynamics Perspective
The semiempirical Hamiltonians MNDO, AM1, PM3, RM1, PDDG/MNDO, PDDG/PM3, and SCC-DFTB, when used as part of a hybrid QM/MM scheme for the simulation of biological molecules, wer...
Publication Info
- Year
- 1983
- Type
- article
- Volume
- 79
- Issue
- 12
- Pages
- 6312-6325
- Citations
- 468
- Access
- Closed
External Links
Social Impact
Altmetric
PlumX Metrics
Social media, news, blog, policy document mentions
Citation Metrics
468
OpenAlex
Cite This
Charles L. Brooks,
Martin Karplus
(1983).
Deformable stochastic boundaries in molecular dynamics.
The Journal of Chemical Physics
, 79
(12)
, 6312-6325.
https://doi.org/10.1063/1.445724
Identifiers
- DOI
- 10.1063/1.445724