Trial distribution functions, dynamic

An MD simulation focusing on the structure and dynamics of both water molecules and counterions around the canonical B-form duplex of d(CGCGCGCG) was reported by Forester and McDonald. These authors used nonbonded interaction parameters from various sources AMBER for DNA atoms, Chandrasekhar et al.i36 parameters for Na+ and Cl, and their own parameters for Ca + ions. Ca + parameters were derived by a trial-and-error method in which peaks in ion-water radial distributions calculated from MC simulations by means of assumed parameters were compared against experimental values. This procedure was repeated adjusting the nonbonded parameters for Ca + until the two radial distribution functions agreed reasonably well. Five different simulations were carried out one on fully charged, polyanionic DNA in pure SPC i water and four on electrically neutral systems... 

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