Paper Citing NAMD - Abstract
Fogolari, Federico; Corazza, Alessandra; Esposito, Gennaro
Accuracy Assessment of the Linear Poisson-Boltzmann Equation and Reparametrization of the OBC Generalized Born Model for Nucleic Acids and Nucleic Acid-Protein Complexes
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:585-596, APR 5 2015
The generalized Born model in the Onufriev, Bashford, and Case (Onufriev et al., Proteins: Struct Funct Genet 2004, 55, 383) implementation has emerged as one of the best compromises between accuracy and speed of computation. For simulations of nucleic acids, however, a number of issues should be addressed: (1) the generalized Born model is based on a linear model and the linearization of the reference Poisson-Boltmann equation may be questioned for highly charged systems as nucleic acids; (2) although much attention has been given to potentials, solvation forces could be much less sensitive to linearization than the potentials; and (3) the accuracy of the Onufriev-Bashford-Case (OBC) model for nucleic acids depends on fine tuning of parameters. Here, we show that the linearization of the Poisson Boltzmann equation has mild effects on computed forces, and that with optimal choice of the OBC model parameters, solvation forces, essential for molecular dynamics simulations, agree well with those computed using the reference Poisson-Boltzmann model. (c) 2015 Wiley Periodicals, Inc.
