2004 Volume 3 Issue 4 Pages 129-136
A new simple implicit solvent model, effective charge (EC) model, was introduced into the Brownian dynamics algorithm based on AMBER united-atom force field. In the EC model, an atomic charge was decreased as a function of solvent-accessible surface area of the atom. We carried out the Brownian dynamics simulations of a 28-mer ββα fold peptide using four implicit solvent models: a generalized Born/solvent-accessible surface area (GB/SA) model, a solvent-accessible surface area (SA) based solvent model, a SA in combination with distance-dependent dielectric (DD/SA) and the EC combined with DD/SA (DD/SA/EC) model; and the calculated results on structure and dynamics of the peptide were compared with those of molecular dynamics simulation using explicit solvent model. Several artifacts were observed in the simulation using the GB/SA model. On the other hand, simulation using the DD/SA and DD/SA/EC implicit solvent models were free from such artifacts. Especially BD with the DD/SA/EC model gave the most stable trajectory as judged by root mean square deviations from the initial structure without large computational cost.
