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

SoftwareX (Jul 2021)

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.

Journal volume & issue: Vol. 15
p. 100749

Abstract

Read online

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.

Published in SoftwareX

ISSN: 2352-7110 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Science: Mathematics: Instruments and machines: Electronic computers. Computer science: Computer software
Website: http://www.journals.elsevier.com/softwarex/

About the journal

Abstract

Keywords