choderalab / pymbar-examplesLinks
Examples of applications of pymbar to various problems in simulation and experiment
☆23Updated 10 years ago
Alternatives and similar repositories for pymbar-examples
Users that are interested in pymbar-examples are comparing it to the libraries listed below
Sorting:
- Temperature generator for Replica Exchange MD simulations☆29Updated 2 years ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆37Updated 2 years ago
- Set up relative free energy calculations using a common scaffold☆24Updated 2 months ago
- ☆30Updated 2 months ago
- Gromacs Implementation of OPLS-AAM Force field☆14Updated 7 years ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆49Updated 4 years ago
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆22Updated 6 years ago
- MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshe…☆23Updated last year
- Different run and analysis scripts as described in the research guides.☆13Updated 3 years ago
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆41Updated last month
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆32Updated 4 months ago
- Q6 Repository -- EVB, FEP and LIE simulator.☆34Updated last year
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆72Updated 2 years ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆31Updated 2 years ago
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆27Updated 5 years ago
- Python code for generating Boresch restraints from MD simulations☆22Updated last week
- Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface☆38Updated 4 years ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆33Updated last year
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆33Updated 4 months ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆28Updated 10 months ago
- Repository for MD methods and analysis from submitted or published work☆19Updated 2 years ago
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆19Updated 2 years ago
- A tutorials suite for BioSimSpace.☆28Updated this week
- ☆39Updated last year
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Updated 6 years ago
- Standalone charge assignment from Espaloma framework.☆41Updated 2 weeks ago
- ☆28Updated last year
- A collections of scripts for working molecular dynamics simulations☆44Updated 2 months ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆17Updated 3 weeks ago
- ☆22Updated 4 months ago