Journal
JOURNAL OF PHYSICAL CHEMISTRY B
Volume 119, Issue 3, Pages 810-823Publisher
AMER CHEMICAL SOC
DOI: 10.1021/jp505332p
Keywords
-
Categories
Funding
- EU FP7 project CRESTA [287703]
- Swedish e-Science Research Center
- Swedish research council [2010-491, 2013-5901]
Ask authors/readers for more resources
Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years several authors have developed increasingly automated procedures to generate parameters for force fields such as Amber, CHARMM, and OPLS. Here, we present a new framework that enables fully automated generation of GROMACS topologies for any of these force fields and an automated setup for parallel adaptive optimization of high-throughput free energy calculation by adjusting lambda point placement on the fly. As a small example of this automated pipeline, we have calculated solvation free energies of 50 different small molecules using the GAFF, OPLS-AA, and CGenFF force fields and four different water models, and by including the often neglected polarization costs, we show that the common charge models are somewhat underpolarized.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available