NNairIITK / Enhanced_Sampling_Methods_Tutorials
Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..
☆40Updated 3 years ago
Related projects: ⓘ
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆30Updated last year
- Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface☆28Updated 2 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆37Updated last year
- A python implementation of the string method with swarms of trajectories using GROMACS☆17Updated last year
- Random Acceleration Molecular Dynamics in GROMACS☆32Updated 2 months ago
- ☆28Updated 3 months ago
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆51Updated last year
- Martini 3 small-molecule database☆54Updated 3 weeks ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆66Updated 3 months ago
- Temperature generator for Replica Exchange MD simulations☆25Updated last year
- ☆38Updated 2 months ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆54Updated last year
- Set up relative free energy calculations using a common scaffold☆18Updated 3 weeks ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated 11 months ago
- A tool for setting up free energy simulations.☆34Updated last year
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆41Updated last month
- PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems☆13Updated 2 years ago
- ☆47Updated last year
- ☆63Updated 8 months ago
- ☆53Updated last year
- ☆25Updated 8 months ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆13Updated last year
- Python implementation of Dynamical Network Analysis☆13Updated last year
- Automatic Mutual Information Noise Omission☆14Updated this week
- Density based object completion over PBC.☆23Updated 11 months ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated 9 months ago
- Machine Learning model for molecular micro-pKa prediction☆29Updated 3 months ago
- ☆11Updated 3 months ago
- Python code for generating Boresch restraints from MD simulations☆17Updated 2 years 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…☆29Updated 7 months ago