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Jansen, Anton, Aho, Noora, Groenhof, Gerrit, Buslaev, Pavel, Hess, Berk (2024) phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS. Journal of Chemical Information and Modeling, 64 (3) 567-574 doi:10.1021/acs.jcim.3c01313

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Reference TypeJournal (article/letter/editorial)
Titlephbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS
JournalJournal of Chemical Information and Modeling
AuthorsJansen, AntonAuthor
Aho, NooraAuthor
Groenhof, GerritAuthor
Buslaev, PavelAuthor
Hess, BerkAuthor
Year2024 (February 12)Volume64
Issue3
PublisherAmerican Chemical Society (ACS)
DOIdoi:10.1021/acs.jcim.3c01313Search in ResearchGate
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Mindat Ref. ID17156788Long-form Identifiermindat:1:5:17156788:7
GUID0
Full ReferenceJansen, Anton, Aho, Noora, Groenhof, Gerrit, Buslaev, Pavel, Hess, Berk (2024) phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS. Journal of Chemical Information and Modeling, 64 (3) 567-574 doi:10.1021/acs.jcim.3c01313
Plain TextJansen, Anton, Aho, Noora, Groenhof, Gerrit, Buslaev, Pavel, Hess, Berk (2024) phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS. Journal of Chemical Information and Modeling, 64 (3) 567-574 doi:10.1021/acs.jcim.3c01313
In(2024, February) Journal of Chemical Information and Modeling Vol. 64 (3) American Chemical Society (ACS)

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Aho, Noora, Groenhof, Gerrit, Buslaev, Pavel (2024) What Is the Protonation State of Proteins in Crystals? Insights from Constant pH Molecular Dynamics Simulations. The Journal of Physical Chemistry B, 128 (45). doi:10.1021/acs.jpcb.4c05947
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Gorelov, Sergey, Titov, Anatoly, Tolicheva, Olga, Konevega, Andrey, Shvetsov, Alexey (2024) DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in Trajectories. Journal of Chemical Information and Modeling, 64 (9) 3593-3598 doi:10.1021/acs.jcim.3c01344
Harris, Robert C., Shen, Jana (2019) GPU-Accelerated Implementation of Continuous Constant pH Molecular Dynamics in Amber: pKa Predictions with Single-pH Simulations. Journal of Chemical Information and Modeling, 59 (11) 4821-4832 doi:10.1021/acs.jcim.9b00754
Van Der Spoel, David, Lindahl, Erik, Hess, Berk, Groenhof, Gerrit, Mark, Alan E., Berendsen, Herman J. C. (2005) GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26 (16). 1701-1718 doi:10.1002/jcc.20291
Panwar, Pawan, Yang, Quanpeng, Martini, Ashlie (2024) Temperature-Dependent Density and Viscosity Prediction for Hydrocarbons: Machine Learning and Molecular Dynamics Simulations. Journal of Chemical Information and Modeling, 64 (7) 2760-2774 doi:10.1021/acs.jcim.3c00231
Sokolovskii, Ilia, Groenhof, Gerrit (2024) Non-Hermitian molecular dynamics simulations of exciton–polaritons in lossy cavities. The Journal of Chemical Physics, 160 (9) doi:10.1063/5.0188613
Yesylevskyy, Semen O. (2007) ProtSqueeze:  Simple and Effective Automated Tool for Setting up Membrane Protein Simulations. Journal of Chemical Information and Modeling, 47 (5) 1986-1994 doi:10.1021/ci600553y
Kührová, Petra, Mlýnský, Vojtěch, Otyepka, Michal, Šponer, Jiří, Banáš, Pavel (2024) Correction to “Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes”. Journal of Chemical Information and Modeling, 64 (13) 5356 doi:10.1021/acs.jcim.4c01067
Berselli, Alessandro, Menziani, Maria Cristina, Muniz-Miranda, Francesco (2024) Structure and Energetics of PET-Hydrolyzing Enzyme Complexes: A Systematic Comparison from Molecular Dynamics Simulations. Journal of Chemical Information and Modeling, 64 (21). doi:10.1021/acs.jcim.4c01369
Páll, Szilárd, Zhmurov, Artem, Bauer, Paul, Abraham, Mark, Lundborg, Magnus, Gray, Alan, Hess, Berk, Lindahl, Erik (2020) Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS. The Journal of Chemical Physics, 153 (13) 134110pp. doi:10.1063/5.0018516
 
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