charmm-gui

There are 8 repositories under charmm-gui topic.

  • bioinfkaustin/gromacs-on-colab

    Google Colab notebooks for running molecular dynamics simulations with GROMACS

    Language:Jupyter Notebook27145

  • cbc-univie/transformato

    Set up relative free energy calculations using a common scaffold

    Language:Python223126

  • nk53/auto_cgui

    Automatic CHARMM-GUI browser interaction with Python

    Language:Python10323
  • addNewResidue.py

    kimjc95/addNewResidue.py

    This code adds custom-made amino acids to the GROMACS forcefield directory.

    Language:Python8203

  • akaupang/macha

    A multi-purpose tool for automated setup of MD systems (e.g. for transformato) and local, menu-based rerunning of CHARMM-GUI input scripts for CHARMM

    Language:Python7103

  • fearlessroad/NAMD_to_CHARMM-GUI

    Tutorial for converting NAMD psf/pdb files to CHARMM PSF/CRD (credit attributed where appropriate to the AMAZING humans who developed these scripts)

    5301

  • aakognole/drude_prepper_analysis

    Analysis scripts for the CHARMM GUI Drude Prepper Paper

    Language:Rich Text Format3301

  • mecomontes/Pyrazinamidase

    A Molecular Dynamics simulation project of pyrazinamidase studying its influence in antibiotic resistance of pyrazinamide. The TIP3P water model as implemented in CHARMM (MacKerell) specifies a 3-site rigid water molecule with charges and Lennard-Jones parameters assigned to each of the 3 atoms. In GROMACS the fix shake command can be used to hold the two O-H bonds and the H-O-H angle rigid. A bond style of harmonic and an angle style of harmonic or charmm should also be used.

    Language:Shell2301