Affiliations: [a] ITS – Research Computing, Northeastern University, Boston, MA 02115, USA | [b] The Charles Stark Draper Laboratory, Cambridge, MA 02139 3563, USA | Tel.: +1 617 258 1515; E-mail: [email protected]
Correspondence:
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Corresponding author: Nilay K. Roy, The Charles Stark Draper Laboratory, Cambridge, MA 02139 3563, USA. Tel.: +1 617 258 1515; E-mail: [email protected].
Abstract: The implementation and results of a new semi-explicit atomistic molecular dynamics simulation method applied to the potassium channel KcsA in a DPPC lipid bilayer and aqueous electrolyte environment is described in detail. For the non-bonded interactions a new and efficient implementation of the original fast multipole method is presented. To obtain the reaction field due to a large implicit lipid bilayer and aqueous electrolyte surrounding the explicit atomic region, a new implementation of the boundary element method valid for the three dielectric interfaces present is used. Rigorous comparisons with known systems that are exactly or numerically solvable are done to check the validity of the implementation method. With the help of detailed force field maps of the reaction field in the channel pore region due to the large implicit lipid bilayer and with the help of the structural changes seen in KcsA we show the importance of this technique. Due to the smaller explicit region now needed numerous runs on large systems are achievable in a reasonable time ensuring good statistics.
Keywords: Boundary element method, fast multipole method, reaction field, Poisson-Boltzmann equation, Debye constant, implicit and explicit regions, Helmholtz layer, molecular dynamics, dielectric interfaces, membrane protein
