J
Jason M. Swails
Researcher at Rutgers University
Publications - 25
Citations - 8625
Jason M. Swails is an academic researcher from Rutgers University. The author has contributed to research in topics: Molecular dynamics & Solvation shell. The author has an hindex of 14, co-authored 25 publications receiving 5410 citations. Previous affiliations of Jason M. Swails include Facultad de Ciencias Exactas y Naturales & University of Florida.
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Journal ArticleDOI
MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.
Bill R. Miller,T. Dwight McGee,Jason M. Swails,Nadine Homeyer,Holger Gohlke,Adrian E. Roitberg +5 more
TL;DR: MMPBSA.py is a program written in Python for streamlining end-state free energy calculations using ensembles derived from molecular dynamics or Monte Carlo simulations, including the Poisson-Boltzmann Model and several implicit solvation models.
Journal ArticleDOI
CHARMM-GUI Input Generator for NAMD, Gromacs, Amber, Openmm, and CHARMM/OpenMM Simulations using the CHARMM36 Additive Force Field
Jumin Lee,Xi Cheng,Jason M. Swails,Min Sun Yeom,Peter Eastman,Justin A. Lemkul,Shuai Wei,Joshua Buckner,Jong Cheol Jeong,Yifei Qi,Sunhwan Jo,Vijay S. Pande,David A. Case,Charles L. Brooks,Alexander D. MacKerell,Jeffery B. Klauda,Wonpil Im +16 more
TL;DR: The optimal simulation protocol for each program has been implemented in CHARMM-GUI and is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.
Journal ArticleDOI
MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
Robert T. McGibbon,Kyle A. Beauchamp,Matthew P. Harrigan,Christoph Klein,Jason M. Swails,Carlos X. Hernández,Christian R. Schwantes,Lee-Ping Wang,Thomas J. Lane,Vijay S. Pande +9 more
TL;DR: MDTraj is a modern, lightweight, and fast software package for analyzing MD simulations that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python.
Journal ArticleDOI
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.
Peter Eastman,Jason M. Swails,John D. Chodera,Robert T. McGibbon,Yutong Zhao,Kyle A. Beauchamp,Lee-Ping Wang,Andrew C. Simmonett,Matthew P. Harrigan,Chaya D. Stern,Rafal P. Wiewiora,Bernard R. Brooks,Vijay S. Pande +12 more
TL;DR: OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility, which makes it an ideal tool for researchers developing new simulation methods, and also allows those new methods to be immediately available to the larger community.
Journal ArticleDOI
Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation
TL;DR: The proposed method for performing constant pH molecular dynamics simulations (CpHMD) in explicit solvent using a discrete protonation state model yields superior predicted pKa values for HEWL over hundreds of nanoseconds of simulation relative to corresponding predicted values from simulations run in implicit solvent.