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gmXtal : Cooking Crystals with GROMACS

Peer-reviewed
Open access
DOI
10.1007/s10930-023-10141-5
Buslaev, Pavel; Groenhof, Gerrit
Protein Journal2024

Scalable Constant pH Molecular Dynamics in GROMACS

Peer-reviewed
Open access
DOI
10.1021/acs.jctc.2c00516
Aho, Noora; Buslaev, Pavel; Jansen, Anton; Bauer, Paul; Groenhof, Gerrit; Hess, Berk
Journal of Chemical Theory and Computation2022

Martini 3 OliGo̅mers:A Scalable Approach for Multimers and Fibrils in GROMACS

Peer-reviewed
Open access
DOI
10.1021/acs.jctc.4c00677
Korshunova, Ksenia; Kiuru, Julius; Liekkinen, Juho; Enkavi, Giray; Vattulainen, Ilpo; Bruininks, Bar...
Journal of Chemical Theory and Computation2024

New QM/MM implementation of the DFTB3 method in the gromacs package

Peer-reviewed
DOI
10.1002/jcc.24029
Kubar, Tomás; Welke, Kai; Groenhof, Gerrit
Journal of Computational Chemistry2015

phbuilder : A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS

Peer-reviewed
Open access
DOI
10.1021/acs.jcim.3c01313
Jansen, Anton; Aho, Noora; Groenhof, Gerrit; Buslaev, Pavel; Hess, Berk
Journal of Chemical Information and Modeling2024

doGlycans-Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS

Peer-reviewed
Open access
DOI
10.1021/acs.jcim.7b00237
Danne, Reinis;Poojari, Chetan;Poojari, Chetan;Martinez-Seara, Hector;Martinez-Seara, Hector;Rissanen...
Journal of chemical information and modeling2017

Topologies, structures and parameter files for lipid simulations in GROMACS with the OPLS-aa force field: DPPC, POPC, DOPC, PEPC, and cholesterol

Peer-reviewed
Open access
DOI
10.1016/j.dib.2015.09.013
Kulig, Waldemar;Pasenkiewicz-Gierula, Marta;Pasenkiewicz-Gierula, Marta;Pasenkiewicz-Gierula, Marta;...
Data in Brief2015

Data including GROMACS input files for atomistic molecular dynamics simulations of mixed, asymmetric bilayers including molecular topologies, equilibrated structures, and force field for lipids compatible with OPLS-AA parameters

Peer-reviewed
Open access
DOI
10.1016/j.dib.2016.03.067
Róg, Tomasz;Róg, Tomasz;Orłowski, Adam;Llorente, Alicia;Skotland, Tore;Sylvänne, Tuulia;Kauhanen, Di...
Data in brief2016

Atomistic Simulation of Ice Nucleation on Silver Iodide (0001) Surfaces with Defects

Peer-reviewed
DOI
10.1021/acs.jpcc.9b08502
Vahabpour Roudsari, Golnaz; Reischl, Bernhard; Pakarinen, Olli Heikki; Vehkamäki, Hanna
Journal of Physical Chemistry C2020

Atomistic and coarse-grained simulations reveal increased ice nucleation activity on silver iodide surfaces in slit and wedge geometries

Peer-reviewed
Open access
DOI
10.5194/acp-22-10099-2022
Vahabpour Roudsari, Golnaz; Pakarinen, Olli Heikki; Reischl, Bernhard; Vehkamäki, Hanna
Atmospheric Chemistry and Physics2022

gmXtal : Cooking Crystals with GROMACS

Peer-reviewed
Open access
DOI
10.1007/s10930-023-10141-5
2024

Scalable Constant pH Molecular Dynamics in GROMACS

Peer-reviewed
Open access
DOI
10.1021/acs.jctc.2c00516
2022

Martini 3 OliGo̅mers:A Scalable Approach for Multimers and Fibrils in GROMACS

Peer-reviewed
Open access
DOI
10.1021/acs.jctc.4c00677
2024

New QM/MM implementation of the DFTB3 method in the gromacs package

Peer-reviewed
DOI
10.1002/jcc.24029
2015

phbuilder : A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS

Peer-reviewed
Open access
DOI
10.1021/acs.jcim.3c01313
2024

doGlycans-Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS

Peer-reviewed
Open access
DOI
10.1021/acs.jcim.7b00237
2017

Topologies, structures and parameter files for lipid simulations in GROMACS with the OPLS-aa force field: DPPC, POPC, DOPC, PEPC, and cholesterol

Peer-reviewed
Open access
DOI
10.1016/j.dib.2015.09.013
2015

Data including GROMACS input files for atomistic molecular dynamics simulations of mixed, asymmetric bilayers including molecular topologies, equilibrated structures, and force field for lipids compatible with OPLS-AA parameters

Peer-reviewed
Open access
DOI
10.1016/j.dib.2016.03.067
2016

Atomistic Simulation of Ice Nucleation on Silver Iodide (0001) Surfaces with Defects

Peer-reviewed
DOI
10.1021/acs.jpcc.9b08502
2020

Atomistic and coarse-grained simulations reveal increased ice nucleation activity on silver iodide surfaces in slit and wedge geometries

Peer-reviewed
Open access
DOI
10.5194/acp-22-10099-2022
2022