Published January 8, 2024 | Version v1
Journal article Open

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

Creators

  • 1. ROR icon KTH Royal Institute of Technology
  • 2. ROR icon University of Jyväskylä

Description

Here, input configurations, topologies, and run parameters for the simulated systems are provided:

* 1cvo_initial (1CVO set up from an initial .pdb)
* 1cvo_converted (1CVO converted from an existing simulation)
* barnase_barstar
* GLIC
* arginine (parameterization and replica runs)

Each directory contains a file script.sh which contains the commands used to set up the system and may be used as a guide.
See also the 'Basic Workflow' and 'Performing Parameterization' sections in the user-manual at https://gitlab.com/gromacs-constantph/phbuilder.

Files

phbuilder_data.zip

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