kzinovjev / string-amberLinks
Adaptive string method implementation in AmberTools23 and Amber22
☆13Updated 11 months ago
Alternatives and similar repositories for string-amber
Users that are interested in string-amber are comparing it to the libraries listed below
Sorting:
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆24Updated 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
- Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems☆15Updated 6 years ago
- Examples of applications of pymbar to various problems in simulation and experiment☆23Updated 10 years ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆28Updated last year
- Quantum Mechanical Bespoke Force Field Derivation Toolkit☆13Updated 5 years ago
- A command line application to launch molecular dynamics simulations with OpenMM☆40Updated 3 years ago
- A tutorials suite for BioSimSpace.☆31Updated 2 months ago
- ☆30Updated last week
- Gromacs Implementation of OPLS-AAM Force field☆14Updated 7 years ago
- Absolute solvation free energy calculations with OpenFF and OpenMM☆25Updated last year
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆27Updated 5 years ago
- MOPAC wrapper providing the PM6-ML correction☆21Updated 5 months ago
- Q6 Repository -- EVB, FEP and LIE simulator.☆35Updated 2 years ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- Different run and analysis scripts as described in the research guides.☆13Updated 3 years ago
- Scripts, inputs and the results generated as part of the training the Sage line of OpenFF force fields.☆21Updated 5 months ago
- Temperature generator for Replica Exchange MD simulations☆29Updated 3 years ago
- NAMD QM/MM Tutorial on Free Energy Profile of Reaction Mechanisms☆13Updated 7 years ago
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Updated 6 years ago
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆15Updated 2 years ago
- Standalone charge assignment from Espaloma framework.☆45Updated 2 months ago
- Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits☆15Updated this week
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆42Updated last month
- Free Parametrization for Small Molecules☆49Updated 2 months 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 6 months ago
- Multiscale Simulation Tool for Backmapping☆22Updated 3 months ago
- ☆34Updated last year
- Notebooks demonstrating how to do simple tasks related to free energy calculations.☆55Updated 2 weeks ago
- Various scripts for quantum chemistry (mainly ORCA)☆14Updated 10 months ago