Update 1.1 to “pysimm: A python package for simulation of molecular systems”, (PII: S2352711016300395)

Demidov, Alexander G.; Perera, B. Lakshitha A.; Fortunato, Michael E.; Lin, Sibo; Colina, Coray M.

doi:10.1016/j.softx.2021.100749

Title: Update 1.1 to “pysimm: A python package for simulation of molecular systems”, (PII: S2352711016300395)

Journal Article · 15 July 2021 · SoftwareX

DOI: https://doi.org/10.1016/j.softx.2021.100749 · OSTI ID:1846187

Demidov, Alexander G. ^[1];

^[2]; Fortunato, Michael E. ^[2];

^[3]; Colina, Coray M. ^[2]

Univ. of Florida, Gainesville, FL (United States); University of Minnesota
Univ. of Florida, Gainesville, FL (United States)
Aramco Research Center, Cambridge, MA (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.

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Research Organization:: Univ. of Minnesota, Minneapolis, MN (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: SC0008688

OSTI ID:: 1846187

Journal Information:: SoftwareX, Journal Name: SoftwareX Vol. 15; ISSN 2352-7110

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (26)

Next generation protein-polymer conjugates Russell, Alan J.; Baker, Stefanie L.; Colina, Coray M. AIChE Journal, Vol. 64, Issue 9 https://doi.org/10.1002/aic.16338	journal	July 2018
Development and testing of a general amber force field Wang, Junmei; Wolf, Romain M.; Caldwell, James W. Journal of Computational Chemistry, Vol. 25, Issue 9 https://doi.org/10.1002/jcc.20035	journal	January 2004
Cassandra: An open source Monte Carlo package for molecular simulation Shah, Jindal K.; Marin-Rimoldi, Eliseo; Mullen, Ryan Gotchy Journal of Computational Chemistry, Vol. 38, Issue 19 https://doi.org/10.1002/jcc.24807	journal	April 2017
Force field for computation of conformational energies, structures, and vibrational frequencies of aromatic polyesters Sun, H. Journal of Computational Chemistry, Vol. 15, Issue 7 https://doi.org/10.1002/jcc.540150708	journal	July 1994
Recent developments and applications of the CHARMM force fields Zhu, Xiao; Lopes, Pedro E. M.; MacKerell, Alexander D. WIREs Computational Molecular Science, Vol. 2, Issue 1 https://doi.org/10.1002/wcms.74	journal	June 2011
Fast Parallel Algorithms for Short-Range Molecular Dynamics Plimpton, Steve Journal of Computational Physics, Vol. 117, Issue 1 https://doi.org/10.1006/jcph.1995.1039	journal	March 1995
Polarizability rescaling and atom-based Thole scaling in the CHARMM Drude polarizable force field for ethers Baker, Christopher M.; MacKerell, Alexander D. Journal of Molecular Modeling, Vol. 16, Issue 3 https://doi.org/10.1007/s00894-009-0572-4	journal	August 2009
Molecular simulation of protein–polymer conjugates Lin, Ping; Colina, Coray M. Current Opinion in Chemical Engineering, Vol. 23 https://doi.org/10.1016/j.coche.2019.02.006	journal	March 2019
pyIAST: Ideal adsorbed solution theory (IAST) Python package Simon, Cory M.; Smit, Berend; Haranczyk, Maciej Computer Physics Communications, Vol. 200 https://doi.org/10.1016/j.cpc.2015.11.016	journal	March 2016
Algorithms and tools for high-throughput geometry-based analysis of crystalline porous materials Willems, Thomas F.; Rycroft, Chris H.; Kazi, Michaeel Microporous and Mesoporous Materials, Vol. 149, Issue 1 https://doi.org/10.1016/j.micromeso.2011.08.020	journal	February 2012
Polymer-enhanced biomacromolecules Kaupbayeva, Bibifatima; Russell, Alan J. Progress in Polymer Science, Vol. 101 https://doi.org/10.1016/j.progpolymsci.2019.101194	journal	February 2020
pysimm: A python package for simulation of molecular systems Fortunato, Michael E.; Colina, Coray M. SoftwareX, Vol. 6 https://doi.org/10.1016/j.softx.2016.12.002	journal	January 2017
Intramolecular Interactions of Conjugated Polymers Mimic Molecular Chaperones to Stabilize Protein–Polymer Conjugates Baker, Stefanie L.; Munasinghe, Aravinda; Murata, Hironobu Biomacromolecules, Vol. 19, Issue 9 https://doi.org/10.1021/acs.biomac.8b00927	journal	August 2018
Materials Informatics with PoreBlazer v4.0 and the CSD MOF Database Sarkisov, Lev; Bueno-Perez, Rocio; Sutharson, Mythili Chemistry of Materials, Vol. 32, Issue 23 https://doi.org/10.1021/acs.chemmater.0c03575	journal	November 2020
CHARMM-GUI Polymer Builder for Modeling and Simulation of Synthetic Polymers Choi, Yeol Kyo; Park, Sang-Jun; Park, Soohyung Journal of Chemical Theory and Computation, Vol. 17, Issue 4 https://doi.org/10.1021/acs.jctc.1c00169	journal	April 2021
Exo -selective, Reductive Heck Derived Polynorbornenes with Enhanced Molecular Weights, Yields, and Hydrocarbon Gas Transport Properties Sundell, Benjamin J.; Lawrence, John A.; Harrigan, Daniel J. ACS Macro Letters, Vol. 9, Issue 9 https://doi.org/10.1021/acsmacrolett.0c00555	journal	August 2020
Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges Vanommeslaeghe, K.; Raman, E. Prabhu; MacKerell, A. D. Journal of Chemical Information and Modeling, Vol. 52, Issue 12 https://doi.org/10.1021/ci3003649	journal	November 2012
Precise Control of Polyolefin Stereochemistry Using Single-Site Metal Catalysts Coates, Geoffrey W. Chemical Reviews, Vol. 100, Issue 4 https://doi.org/10.1021/cr990286u	journal	April 2000
DREIDING: a generic force field for molecular simulations Mayo, Stephen L.; Olafson, Barry D.; Goddard, William A. The Journal of Physical Chemistry, Vol. 94, Issue 26, p. 8897-8909 https://doi.org/10.1021/j100389a010	journal	December 1990
Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K Mark, Pekka; Nilsson, Lennart The Journal of Physical Chemistry A, Vol. 105, Issue 43 https://doi.org/10.1021/jp003020w	journal	November 2001
A Polarizable Force Field of Dipalmitoylphosphatidylcholine Based on the Classical Drude Model for Molecular Dynamics Simulations of Lipids Chowdhary, Janamejaya; Harder, Edward; Lopes, Pedro E. M. The Journal of Physical Chemistry B, Vol. 117, Issue 31 https://doi.org/10.1021/jp402860e	journal	July 2013
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins ^† MacKerell, A. D.; Bashford, D.; Bellott, M. The Journal of Physical Chemistry B, Vol. 102, Issue 18 https://doi.org/10.1021/jp973084f	journal	April 1998
Structure–function–dynamics of α-chymotrypsin based conjugates as a function of polymer charge Munasinghe, Aravinda; Baker, Stefanie L.; Lin, Ping Soft Matter, Vol. 16, Issue 2 https://doi.org/10.1039/C9SM01842E	journal	January 2020
A modified TIP3P water potential for simulation with Ewald summation Price, Daniel J.; Brooks, Charles L. The Journal of Chemical Physics, Vol. 121, Issue 20 https://doi.org/10.1063/1.1808117	journal	November 2004
Comparison of simple potential functions for simulating liquid water Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D. The Journal of Chemical Physics, Vol. 79, Issue 2 https://doi.org/10.1063/1.445869	journal	July 1983
A molecular dynamics study of water-soluble polymers: analysis of force fields from atomistic simulations Rukmani, Shalini J.; Kupgan, Grit; Anstine, Dylan M. Molecular Simulation, Vol. 45, Issue 4-5 https://doi.org/10.1080/08927022.2018.1531401	journal	October 2018

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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
97 MATHEMATICS AND COMPUTING
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Pysimm

Title: Update 1.1 to “pysimm: A python package for simulation of molecular systems”, (PII: S2352711016300395)

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