Kremer–Grest polymer simulation dataset: 20 beads per chain, 8000 total beads, max alpha time 10^7, data from Hung et al., 2018
Description
Summary: This dataset contains molecular dynamics simulation inputs, outputs, and selected analysis data for an attractive Kremer-Grest bead-spring polymer glass-former. The simulations were first reported in: Hung, J.-H., Patra, T. K., Meenakshisundaram, V., Mangalara, J. H. & Simmons, D. S. Universal localization transition accompanying glass formation: insights from efficient molecular dynamics simulations of diverse supercooled liquids. Soft Matter 15, 1223-1242 (2018). That publication and this dataset should be cited in any publication using these data. Simulated system: The system is an attractive Kremer-Grest bead-spring polymer with 12-6 Lennard-Jones interactions truncated at 2.5 sigma, 8000 total beads, and 20 beads per chain, simulated at a constant pressure of 0. Simulations targeted alpha relaxation times approaching 10^7 Lennard-Jones time units. The thermal protocol was based on the Predictive Stepwise Quench Algorithm (PreSQ). This dataset merges elements of two independent runs of that protocol, denoted 000 and 001. Contents: The archive includes simulation inputs and outputs for generation, quench, equilibration, and production elements, together with selected analysis data. The simulations/ directory contains workflow subdirectories, Packmol inputs, and LAMMPS input templates. Production outputs are in simulations/production/ and include exponentially spaced custom LAMMPS trajectories collected during isothermal production simulations. Production trajectories are provided as a compressed tarball. For users wishing to simply make use of these trajectories to study the system's physics, these will be the most important files, together with the associated production log files specifying the time scheme. Trajectories from other simulation elements are provided in compressed LAMMPS xyz tarballs. Analysis results generated using AMDAT are in the analysis/ directory. The AMDAT analysis package, which can be readily used to further analyze these files, can be found here: https://github.com/dssimmons-codes/AMDAT. Temperatures are encoded in filenames as a 6- to 7-digit number following the capital letter T; the reduced Lennard-Jones temperature is obtained by dividing this number by 1,000,000. Additional documentation, including directory structure, file conventions, and interpretation of equilibrium status, is provided in the dataset README. Caution: Not all temperatures with archived outputs are necessarily in equilibrium. Temperatures identified by PreSQ as satisfying equilibrium criteria are listed in analysis/fit_data. For each replicate, the Regime8 file reports the temperatures and relaxation times accepted as in equilibrium.
Files
Institutions
- University of South FloridaFlorida, Tampa
Categories
Funders
- U.S. National Science FoundationGovernment of the United States of AmericaAlexandriaGrant ID: DMR - 1554920
- W. M. Keck FoundationLos Angeles