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11 results in Keywords: GROMACS

Physical Chemistry

Working Paper

Making Soup: Preparing and Validating Molecular Simulations of the Bacterial Cytoplasm

Leandro Oliveira Bortot, Zahedeh Bashardanesh, David van der Spoel

Version 1 posted 06 November 2019

672

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Theoretical and Computational Chemistry

Working Paper

Phase-Transferable Force Field for Alkali Halides

Marie-Madeleine Walz, Mohammad Ghahremanpour, Paul J. van Maaren, David van der Spoel

Version 1 posted 10 September 2018

862

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Physical Chemistry

Working Paper

NMR Refinement and Peptide Folding Using the GROMACS Software

Anna Sinelnikova, David van der Spoel

Version 1 posted 27 January 2021

338

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Theoretical and Computational Chemistry

Working Paper

ASGARD. A simple and automatic GROMACS tool to analyze Molecular Dynamic simulations

Alejandro Rodríguez-Martínez, Jochem Nelen, Miguel Carmena-Bargueño, Carlos Martínez-Cortés, Irene Luque, Horacio Pérez-Sánchez

Version 1 posted 14 February 2023

1,140

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Theoretical and Computational Chemistry

Working Paper

phbuilder: a tool for efficiently setting up constant pH molecular dynamics simulations in GROMACS

Anton Jansen, Noora Aho, Gerrit Groenhof, Pavel Buslaev, Berk Hess

Version 1 posted 11 August 2023

692

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Theoretical and Computational Chemistry

Working Paper

Gromologist: a Gromacs-Oriented Utility Library for Structure and Topology Manipulation

Milosz Wieczor, Jacek Czub

Version 1 posted 24 May 2022

402

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Citations

Theoretical and Computational Chemistry

Working Paper

Neighbor List Artifacts in Molecular Dynamics Simulations

HYUNTAE KIM, Balázs Fábián, Gerhard Hummer

Version 1 posted 18 July 2023

1,619

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Citations

Chemical Engineering and Industrial Chemistry

Working Paper

Molecular Modelling of Ionic Liquids: General Guidelines on Fixed-Charge Force Fields for Balanced Descriptions

Zhaoxi Sun, Zhihao Gong, Lei Zheng, Payam Kalhor, Zhe Huai, Zhirong Liu

Version 2 posted 30 June 2022

442

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Theoretical and Computational Chemistry

Working Paper

Scalable Constant pH Molecular Dynamics in GROMACS

Noora Aho, Pavel Buslaev, Anton Jansen, Paul Bauer, Gerrit Groenhof, Berk Hess

Version 2 posted 27 January 2022

2,171

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Citations

Theoretical and Computational Chemistry

Working Paper

Best practices in constant pH MD simulations: accuracy and sampling

Pavel Buslaev, Noora Aho, Anton Jansen, Paul Bauer, Berk Hess, Gerrit Groenhof

Version 1 posted 18 May 2022

556

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11 results in GROMACS in Keywords: GROMACS

Making Soup: Preparing and Validating Molecular Simulations of the Bacterial Cytoplasm

Phase-Transferable Force Field for Alkali Halides

NMR Refinement and Peptide Folding Using the GROMACS Software

ASGARD. A simple and automatic GROMACS tool to analyze Molecular Dynamic simulations

phbuilder: a tool for efficiently setting up constant pH molecular dynamics simulations in GROMACS

Gromologist: a Gromacs-Oriented Utility Library for Structure and Topology Manipulation

Neighbor List Artifacts in Molecular Dynamics Simulations

Molecular Modelling of Ionic Liquids: General Guidelines on Fixed-Charge Force Fields for Balanced Descriptions

Scalable Constant pH Molecular Dynamics in GROMACS

Best practices in constant pH MD simulations: accuracy and sampling

11 results in Keywords: GROMACS