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Incorporating solvent and ion screening into molecular dynamics using the finite‐difference Poisson–Boltzmann method
Author(s) -
Sharp Kim
Publication year - 1991
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540120407
Subject(s) - solvation , molecular dynamics , force field (fiction) , chemistry , poisson–boltzmann equation , ion , solvent , computational chemistry , molecule , solvent effects , computation , chemical physics , solvent models , implicit solvation , statistical physics , physics , computer science , quantum mechanics , organic chemistry , algorithm
The finite difference method for solving the Poisson–Boltzmann equation is used to calculate the reaction field acting on a macromolecular solute due to the surrounding water and ions. Comparisons with analytical test cases indicate that the solvation forces can be calculated rapidly and accurately with this method. These forces act to move charged solute atoms towards the solvent where they are better solvated, and to screen interactions between charges. A way of combining such calculations with conventional molecular dynamics force fields is proposed which requires little modification of existing molecular dynamics programs. Simulations on the alanine dipeptide show that solvent forces affect the conformational dynamics by reducing the preference for internal H‐bonding forms, increasing the R ‐alpha helix preference and reducing transition barriers. These solvent effects are similar to previous explicit solvent simulations, but require little more computation than vacuum simulations. The method should scale up with little increase in computational cost to larger molecules such as proteins and nucleic acids.