callumjd / AMBER-Umbrella_COM_restraint_tutorial
Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane
☆30Updated last year
Alternatives and similar repositories for AMBER-Umbrella_COM_restraint_tutorial:
Users that are interested in AMBER-Umbrella_COM_restraint_tutorial are comparing it to the libraries listed below
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆43Updated 3 years ago
- Different run and analysis scripts as described in the research guides.☆12Updated 2 years ago
- Temperature generator for Replica Exchange MD simulations☆27Updated 2 years ago
- Set up relative free energy calculations using a common scaffold☆22Updated 5 months ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- An OpenMM plugin that implements the Alchemical Transfer Potential☆37Updated last year
- Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface☆33Updated 3 years ago
- Q6 Repository -- EVB, FEP and LIE simulator.☆31Updated last year
- PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems☆13Updated 3 years ago
- A python implementation of the string method with swarms of trajectories using GROMACS☆18Updated 2 years ago
- ☆26Updated last year
- ☆54Updated last year
- ☆39Updated 6 months ago
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆56Updated last year
- Random Acceleration Molecular Dynamics in GROMACS☆34Updated 6 months ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆14Updated last year
- ☆26Updated 7 months ago
- scripts for analyzing molecular dynamics trajectories using VMD☆38Updated 9 years ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆63Updated last year
- A tool for setting up free energy simulations.☆35Updated 2 years ago
- Analysis of non-covalent interactions in MD trajectories☆51Updated 3 weeks ago
- Advanced toolkit for binding free energy calculations☆32Updated 3 weeks 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 collections of scripts for working molecular dynamics simulations☆41Updated 8 months ago
- Yasara plugins for Gromacs users☆25Updated last year
- Density based object completion over PBC.☆27Updated last month
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆45Updated 2 months ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆74Updated 7 months ago
- ☆25Updated last year
- ☆29Updated 3 months ago