RagnarB83 / chemshell-QMMM-protein-setup
MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshell) and the ORCA code as QM code for Chemshell.)
☆22Updated 11 months ago
Alternatives and similar repositories for chemshell-QMMM-protein-setup
Users that are interested in chemshell-QMMM-protein-setup are comparing it to the libraries listed below
Sorting:
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆29Updated last year
- PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems☆15Updated 3 years ago
- ☆35Updated 8 months ago
- Temperature generator for Replica Exchange MD simulations☆28Updated 2 years ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆15Updated last year
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆45Updated 4 years ago
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆22Updated 5 years ago
- Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface☆35Updated 3 years ago
- Gromacs Implementation of OPLS-AAM Force field☆13Updated 6 years ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆32Updated last year
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Updated 2 years ago
- A collections of scripts for working molecular dynamics simulations☆43Updated 11 months ago
- Density based object completion over PBC.☆29Updated 5 months ago
- Examples of applications of pymbar to various problems in simulation and experiment☆21Updated 10 years ago
- Different run and analysis scripts as described in the research guides.☆13Updated 2 years ago
- Python code for generating Boresch restraints from MD simulations☆20Updated 2 years ago
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆24Updated 5 years ago
- Enhanced sampling methods for molecular dynamics simulations☆36Updated 2 years ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- A tutorials suite for BioSimSpace.☆25Updated 2 weeks ago
- ☆21Updated 8 months ago
- Q6 Repository -- EVB, FEP and LIE simulator.☆31Updated last year
- The pDynamo molecular modeling and simulation program☆37Updated 2 weeks ago
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆32Updated 5 years ago
- Lee-Ping's general purpose script for running OpenMM molecular dynamics simulations☆28Updated last year
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- GridMAT-MD membrane analysis program☆24Updated 6 years ago
- Repository of the data for PLUMED Masterclass 22.3☆13Updated 10 months ago
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆31Updated last month