Role of Counterions in Constant-pH Molecular Dynamics Simulations of PAMAM Dendrimers.

ABSTRACT: Electrostatic interactions play a pivotal role in the structure and mechanism of action of most biomolecules. There are several conceptually different methods to deal with electrostatics in molecular dynamics simulations. Ionic strength effects are usually introduced using such methodologies and can have a significant impact on the quality of the final conformation space obtained. We have previously shown that full system neutralization can lead to wrong lipidic phases in the 25% PA/PC bilayer (J. Chem. Theory Comput. 2014,10, 5483-5492). In this work, we investigate how two limit approaches to the ionic strength treatment (implicitly with GRF or using full system neutralization with either GRF or PME) can influence the conformational space of the second-generation PAM

SUBMITTER: Reis PBPS 

PROVIDER: S-EPMC6045380 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature