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A smooth particle mesh Ewald method
- U. Essmann, L. Perera, M. Berkowitz, T. Darden, Hsing-Chou Lee, L. Pedersen
- Computer Science
- 15 November 1995
It is demonstrated that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N), which is comparable to that of a simple truncation method of 10 A or less.
Ewald summation for systems with slab geometry
We propose a modification in the three-dimensional Ewald summation technique for calculations of long-range Coulombic forces for systems with a slab geometry that are periodic in two dimensions and…
Molecular dynamics simulation of sodium dodecyl sulfate micelle in water: Micellar structural characteristics and counterion distribution
An all-atom 5 nanosecond molecular dynamics simulation of a water-solvated micelle containing 60 sodium dodecyl sulfate monomers was performed. Structural properties such as the radius of gyration,…
Molecular dynamics simulation of a dipalmitoylphosphatidylcholine bilayer with NaCl.
Molecular dynamics simulations of sodium dodecyl sulfate micelle in water: The behavior of water
Using a 5 ns explicit atom molecular dynamics simulation of a 60 monomer sodium dodecyl sulfate micellar system containing 7579 TIP3P water molecules, the behavior of water in different electrostatic…
Effects of alkali cations and halide anions on the DOPC lipid membrane.
The simulations revealed that sodium is attracted to the headgroup region with its concentration being maximal in the vicinity of the phosphate groups, this effect being likely underestimated within the present nonpolarizable force field.
The origin of the hydration interaction of lipid bilayers from MD simulation of dipalmitoylphosphatidylcholine membranes in gel and liquid crystalline phases
The results of four molecular dynamics simulations of dipalmitoylphosphatidylcholine (DPPC)/water systems are reported. To investigate the origin of the hydration force we follow the experiments…
Molecular dynamics simulation of the structure of dimyristoylphosphatidylcholine bilayers with cholesterol, ergosterol, and lanosterol.
Exterior site occupancy infers chloride-induced proton gating in a prokaryotic homolog of the ClC chloride channel.
Details of this gating mechanism are inferred by studying the free energetics of Cl(-) occupancy in the pore of a prokaryotic ClC homolog by inducing the conserved glutamate's protonation.
Aqueous solutions next to phospholipid membrane surfaces: insights from simulations.
It is well established that water plays a very important role in the functioning of biological molecules and their assemblies and contributes to the assisted passage of ions and other molecules across membranes through special membrane-embedded proteins.