Lignin Forcefield Source Datafiles

Three archives are provided here comprising the development of a CHARMM36-compatible lignin forcefield suitable for use in biomolecular simulations. One archive parameters.zip contains the output topology and parameter files in CHARMM format suitable for use in constructing simulation systems. The remaining two hold the logic of the parameterization featuring scripts that do the optimization including the source for the GPU-accelerated objective function evaluation and target data creation scripts.zip as well as minimal outputs needed to recreate the work datafiles.zip. Due to licensing restrictions Gaussian log files that created the target data are not provided here. Instead only binary-formatted parsed target data as well as the input decks used to create the target data are provided in datafiles.zip. Readme files for individual directories created within the directory structure are contained within scripts.zip.
4 Resources
Name Size Type Resource Description
parameters.zip 14.94 KB Archive Topology and parameter files in CHARMM format, suitable for use in constructing simulation systems
scripts.zip 620.02 KB Archive Scripts that were used to do the optimization (including the source for the GPU-accelerated objective function evaluation) and target data creation.
datafiles.zip 166.71 MB Archive Minimal outputs needed by the scripts included in scripts.zip to demonstrate functionality and the assumptions used.
Dataset link 0 KB Website Lignin parameterization dataset hosted by the CSC.
Author Information
Michael Crowley, National Renewable Energy Laboratory, ORCID iD: 0000-0001-5163-9398
Joshua Vermaas, National Renewable Energy Laboratory, ORCID iD: 0000-0003-3139-6469
Gregg Beckham, National Renewable Energy Laboratory, ORCID iD: 0000-0002-3480-212X
Cite This Dataset
Crowley, Michael; Vermaas, Joshua; Beckham, Gregg (2018): Lignin Forcefield Source Datafiles. National Renewable Energy Laboratory. https://data.nrel.gov/submissions/82
About This Dataset
82
70925
Public
04/30/2018
Facilities
High Performance Computing Center (HPC)
Sponsoring Organization
National Renewable Energy Laboratory
Research Areas
Chemistry
Computational Science