MayLab-UConn / BUMPy
☆23Updated 3 years ago
Alternatives and similar repositories for BUMPy:
Users that are interested in BUMPy are comparing it to the libraries listed below
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆30Updated last year
- Materials for the 2021 PRACE Workshop @ SurfSARA☆31Updated 3 years ago
- Temperature generator for Replica Exchange MD simulations☆27Updated 2 years ago
- Gromacs Implementation of OPLS-AAM Force field☆13Updated 6 years ago
- Set up relative free energy calculations using a common scaffold☆22Updated 6 months ago
- Density based object completion over PBC.☆27Updated 3 months ago
- A python implementation of the string method with swarms of trajectories using GROMACS☆18Updated 2 years ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆66Updated last year
- Analysis of non-covalent interactions in MD trajectories☆53Updated 2 months ago
- Python code for generating Boresch restraints from MD simulations☆19Updated 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..☆44Updated 4 years ago
- Q6 Repository -- EVB, FEP and LIE simulator.☆31Updated last year
- Automatic Mutual Information Noise Omission☆14Updated 5 months ago
- Program for robust fitting of bonded Molecular Mechanics parameters☆15Updated 9 years ago
- ☆33Updated 6 months ago
- A tutorials suite for BioSimSpace.☆24Updated 2 weeks ago
- A simple implementation of replica exchange MD simulations for OpenMM.☆23Updated 3 years ago
- Compare optimized geometries and energies from various force fields with respect to a QM reference.☆13Updated 3 years ago
- Robust Equilibration Detection☆19Updated 3 weeks ago
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆24Updated 4 years ago
- ☆26Updated this week
- Fast PBC wrapping and unwrapping for VMD☆23Updated 3 months ago
- GridMAT-MD membrane analysis program☆24Updated 6 years ago
- ☆26Updated last year
- Examples of applications of pymbar to various problems in simulation and experiment☆20Updated 10 years ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- 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 year
- PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems☆13Updated 3 years ago