gpantel / MD_methods-and-analysisLinks
Repository for MD methods and analysis from submitted or published work
☆19Updated 2 years ago
Alternatives and similar repositories for MD_methods-and-analysis
Users that are interested in MD_methods-and-analysis are comparing it to the libraries listed below
Sorting:
- Examples of applications of pymbar to various problems in simulation and experiment☆23Updated 10 years ago
- Enhanced sampling methods for molecular dynamics simulations☆38Updated 2 years ago
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆22Updated 5 years ago
- Absolute solvation free energy calculations with OpenFF and OpenMM☆23Updated 8 months ago
- Temperature generator for Replica Exchange MD simulations☆29Updated 2 years ago
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆25Updated 5 years ago
- A Package for Parametrization of Molecular Mechanics Force Fields☆33Updated 2 years ago
- Conformer-Rotamer Ensemble Sampling Tool based on the xtb Semiempirical Extended Tight-Binding Program Package☆36Updated last month
- Scripts, inputs and the results generated as part of the training the Sage line of OpenFF force fields.☆21Updated last month
- Gromacs Implementation of OPLS-AAM Force field☆14Updated 7 years ago
- Automated reaction discovery and dataset generation with the growing string method☆20Updated 5 years ago
- ☆12Updated last month
- ☆38Updated 11 months ago
- Equivariant GNN for the prediction of atomic multipoles up to quadrupoles.☆30Updated 3 years ago
- Package for consistent reporting of relative free energy results☆39Updated 2 months ago
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆29Updated last year
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆40Updated last month
- A simple implementation of replica exchange MD simulations for OpenMM.☆24Updated 4 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
- Implicit Solvent Approach Based on Generalised Born and Transferable Graph Neural Networks for Molecular Dynamics Simulations☆48Updated 3 months ago
- Materials for the 2021 PRACE Workshop @ SurfSARA☆30Updated 3 years ago
- Ensembler is a python package that provides fast and easy access to 1D and 2D model system simulations. It can be used for method develop…☆53Updated last year
- ☆65Updated last month
- ☆17Updated 10 months ago
- Using supervised machine learning to build collective variables for accelerated sampling☆28Updated 7 years ago
- Standalone charge assignment from Espaloma framework.☆40Updated last year
- ☆12Updated last year
- Set up relative free energy calculations using a common scaffold☆24Updated last week
- A Python library for constructing polymer topologies and coordinates☆12Updated last month
- Transferable Double Exponential non-bonded potential for condensed phase simulations of small molecules☆23Updated last year