Update 1.1 to “pysimm: A python package for simulation of molecular systems”, (PII: S2352711016300395)
Alexander G. Demidov,
B. Lakshitha A. Perera,
Michael E. Fortunato,
Sibo Lin,
Coray M. Colina
Affiliations
Alexander G. Demidov
Department of Chemistry, University of Florida, Gainesville, FL 32611, United States; George and Josephine Butler Polymer Research Laboratory, University of Florida, Gainesville, FL 32611, United States; Center for Macromolecular Science & Engineering, University of Florida, Gainesville, FL 32611, United States
B. Lakshitha A. Perera
Department of Chemistry, University of Florida, Gainesville, FL 32611, United States; George and Josephine Butler Polymer Research Laboratory, University of Florida, Gainesville, FL 32611, United States; Center for Macromolecular Science & Engineering, University of Florida, Gainesville, FL 32611, United States
Michael E. Fortunato
Department of Chemistry, University of Florida, Gainesville, FL 32611, United States; George and Josephine Butler Polymer Research Laboratory, University of Florida, Gainesville, FL 32611, United States; Center for Macromolecular Science & Engineering, University of Florida, Gainesville, FL 32611, United States
Sibo Lin
Aramco Services Company: Aramco Research Center — Boston, 400 Technology Square, Cambridge, MA, 02139, United States
Coray M. Colina
Department of Chemistry, University of Florida, Gainesville, FL 32611, United States; George and Josephine Butler Polymer Research Laboratory, University of Florida, Gainesville, FL 32611, United States; Center for Macromolecular Science & Engineering, University of Florida, Gainesville, FL 32611, United States; Department of Materials Science and Engineering, University of Florida, Gainesville, FL 32611, United States; Corresponding author at: Department of Chemistry, University of Florida, Gainesville, FL 32611, United States.
This update of the pysimm application programming interface, pysimm 1.1, provides both infrastructural as well as functional updates. Moreover, improvements to the random walk application that allow it to construct polymers with controlled tacticity are highlighted. Additions to the forcefield module include an update to enable working with the family of CHARMM forcefields and automated typing with the CHARMM generalized forcefield (CGenFF). Finally, new detailed examples demonstrating new features are also provided.
