Development of a lattice-sum method emulating nonperiodic boundary conditions for the treatment of electrostatic interactions in molecular simulations: A continuum-electrostatics study

2006 ◽  
Vol 124 (12) ◽  
pp. 124108 ◽  
Author(s):  
Mika A. Kastenholz ◽  
Philippe H. Hünenberger
Keyword(s):  
Boundary Conditions ◽  
Electrostatic Interactions ◽  
Molecular Simulations ◽  
Continuum Electrostatics ◽  
Lattice Sum

Lattice‐sum methods for calculating electrostatic interactions in molecular simulations

1995 ◽  
Vol 103 (8) ◽  
pp. 3014-3021 ◽  
Author(s):  
Brock A. Luty ◽  
Ilario G. Tironi ◽  
Wilfred F. van Gunsteren
Keyword(s):  
Electrostatic Interactions ◽  
Molecular Simulations ◽  
Lattice Sum

Characterizing the Water Wire in the Gramicidin Channel Found by Monte Carlo Sampling Using Continuum Electrostatics and in Molecular Dynamics Trajectories with Conventional or Polarizable Force Fields

2020 ◽  
pp. 1-20
Author(s):  
Yingying Zhang ◽  
Kamran Haider ◽  
Divya Kaur ◽  
Van A. Ngo ◽  
Xiuhong Cai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Dipole Moment ◽  
Electrostatic Interactions ◽  
Hybrid Methods ◽  
Force Fields ◽  
Proton Channel ◽  
Water Molecules ◽  
Implicit Solvent ◽  
Continuum Electrostatics ◽  
Hydrogen Bond Networks

Water molecules play a key role in all biochemical processes. They help define the shape of proteins, and they are reactant or product in many reactions and are released as ligands are bound. They facilitate the transfer of protons through transmembrane proton channel, pump and transporter proteins. Continuum electrostatics (CE) force fields used by program Multiconformation CE (MCCE) capture electrostatic interactions in biomolecules with an implicit solvent, which captures the averaged solvent water equilibrium properties. Hybrid CE methods can use explicit water molecules within the protein surrounded by implicit solvent. These hybrid methods permit the study of explicit hydrogen bond networks within the protein and allow analysis of processes such as proton transfer reactions. Yet hybrid CE methods have not been rigorously tested. Here, we present an explicit treatment of water molecules in the Gramicidin A (gA) channel using MCCE and compare the resulting distributions of water molecules and key hydration features against those obtained with explicit solvent Molecular Dynamics (MD) simulations with the nonpolarizable CHARMM36 and polarizable Drude force fields. CHARMM36 leads to an aligned water wire in the channel characterized by a large absolute net water dipole moment; the MCCE and Drude analysis lead to a small net dipole moment as the water molecules change orientation within the channel. The correct orientation is not as yet known, so these calculations identify an open question.

scholarly journals Electrostatically controlled surface boundary conditions in nematic liquid crystals and colloids

2019 ◽  
Vol 5 (9) ◽  
pp. eaax4257 ◽  
Author(s):  
Haridas Mundoor ◽  
Bohdan Senyuk ◽  
Mahmoud Almansouri ◽  
Sungoh Park ◽  
Blaise Fleury ◽  
...  
Keyword(s):  
Liquid Crystals ◽  
Boundary Conditions ◽  
Electrostatic Interactions ◽  
Surface Boundary ◽  
Anisotropic Particles ◽  
Surface Alignment ◽  
Surface Charging ◽  
Surface Boundary Conditions ◽  
Anisotropic Elastic ◽  
Colloidal Inclusions

Differing from isotropic fluids, liquid crystals exhibit highly anisotropic interactions with surfaces, which define boundary conditions for the alignment of constituent rod-like molecules at interfaces with colloidal inclusions and confining substrates. We show that surface alignment of the nematic molecules can be controlled by harnessing the competing aligning effects of surface functionalization and electric field arising from surface charging and bulk counterions. The control of ionic content in the bulk and at surfaces allows for tuning orientations of shape-anisotropic particles like platelets within an aligned nematic host and for changing the orientation of director relative to confining substrates. The ensuing anisotropic elastic and electrostatic interactions enable colloidal crystals with reconfigurable symmetries and orientations of inclusions.

scholarly journals Image Charge Method for Reaction Fields in a Hybrid Ion-Channel Model

2011 ◽  
Vol 9 (4) ◽  
pp. 1056-1070 ◽  
Author(s):  
Zhenli Xu ◽  
Wei Cai ◽  
Xiaolin Cheng
Keyword(s):  
Boundary Conditions ◽  
Ion Channel ◽  
Electrostatic Interactions ◽  
Channel Model ◽  
Field Potential ◽  
Image Method ◽  
Optimization Approach ◽  
Inhomogeneous System ◽  
Reaction Field ◽  
Ion Channel Model

AbstractA multiple-image method is proposed to approximate the reaction-field potential of a source charge inside a finite length cylinder due to the electric polarization of the surrounding membrane and bulk water. When applied to a hybrid ion-channel model, this method allows a fast and accurate treatment of the electrostatic interactions of protein with membrane and solvent. To treat the channel/membrane interface boundary conditions of the electric potential, an optimization approach is used to derive image charges by fitting the reaction-field potential expressed in terms of cylindric harmonics. Meanwhile, additional image charges are introduced to satisfy the boundary conditions at the planar membrane interfaces. In the end, we convert the electrostatic interaction problem in a complex inhomogeneous system of ion channel/membrane/water into one in a homogeneous free space embedded with discrete charges (the source charge and image charges). The accuracy of this method is then validated numerically in calculating the solvation self-energy of a point charge.

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