GitHub topics: charmm-gui
Adam-maz/Toolkit-for-NAMD
I present tools that accelerate molecular dynamics (MD) simulations using NAMD software and support the analysis of the obtained trajectories.
Language: Jupyter Notebook - Size: 29.2 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0
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)
Size: 12.7 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 6 - Forks: 1
cbc-univie/transformato
Set up relative free energy calculations using a common scaffold
Language: Python - Size: 209 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 22 - Forks: 6
kimjc95/addNewResidue.py
This code adds custom-made amino acids to the GROMACS forcefield directory.
Language: Python - Size: 2.79 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 8 - Forks: 2
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: Shell - Size: 281 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 1
bioinfkaustin/gromacs-on-colab
Google Colab notebooks for running molecular dynamics simulations with GROMACS
Language: Jupyter Notebook - Size: 25.4 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 8 - Forks: 3
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: Python - Size: 4.62 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 3
nk53/auto_cgui
Automatic CHARMM-GUI browser interaction with Python
Language: Python - Size: 89.3 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 3
aakognole/drude_prepper_analysis
Analysis scripts for the CHARMM GUI Drude Prepper Paper
Language: Rich Text Format - Size: 30.9 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 1
