Assessing the Current State of Amber Force Field Modifications for DNA.

ABSTRACT: The utility of molecular dynamics (MD) simulations to model biomolecular structure, dynamics, and interactions has witnessed enormous advances in recent years due to the availability of optimized MD software and access to significant computational power, including GPU multicore computing engines and other specialized hardware. This has led researchers to routinely extend conformational sampling times to the microsecond level and beyond. The extended sampling time has allowed the community not only to converge conformational ensembles through complete sampling but also to discover deficiencies and overcome problems with the force fields. Accuracy of the force fields is a key component, along with sampling, toward being able to generate accurate and stable structures of biopolymers. The Ambe

SUBMITTER: Galindo-Murillo R 

PROVIDER: S-EPMC4980684 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature