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
- ☆30Updated last month
- Gromacs Implementation of OPLS-AAM Force field☆14Updated 7 years ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 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
- 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
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆49Updated 4 years ago
- Set up relative free energy calculations using a common scaffold☆24Updated 3 weeks 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…☆32Updated 3 months ago
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆25Updated 5 years ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆31Updated last year
- ☆39Updated last year
- Q6 Repository -- EVB, FEP and LIE simulator.☆34Updated last year
- Repository for MD methods and analysis from submitted or published work☆19Updated 2 years ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆17Updated last week
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆19Updated 2 years ago
- Package for consistent reporting of relative free energy results☆39Updated last week
- A tutorials suite for BioSimSpace.☆26Updated 4 months ago
- ☆28Updated last year
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆40Updated last week
- RESP with inter- and intra-molecular constraints in Psi4.☆32Updated 2 years ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- Absolute solvation free energy calculations with OpenFF and OpenMM☆23Updated 9 months ago
- Scripts, inputs and the results generated as part of the training the Sage line of OpenFF force fields.☆21Updated 2 months ago
- User Guide for MDAnalysis☆27Updated this week
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆28Updated 9 months ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆72Updated 2 years ago
- Enhanced sampling methods for molecular dynamics simulations☆38Updated 2 years ago
- Conformer-Rotamer Ensemble Sampling Tool based on the xtb Semiempirical Extended Tight-Binding Program Package☆35Updated last month
- ☆10Updated 5 years ago