msultan / tf_metadynamics
Using neural networks for enhanced sampling in computational biophysics
☆15Updated 7 years ago
Related projects: ⓘ
- scripts for analyzing molecular dynamics trajectories using VMD☆35Updated 9 years ago
- Database of hand-built OPLS-AA parameters and topologies for 464 molecules. Zip files contains parameter and topologies for OpenMM, Groma…☆31Updated 6 years ago
- Examples of applications of pymbar to various problems in simulation and experiment☆16Updated 9 years ago
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆17Updated 4 years ago
- ☆13Updated 5 years ago
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆26Updated 4 years ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆30Updated last year
- ☆15Updated 7 years ago
- Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface☆28Updated 2 years ago
- Calculation of water/solvent partition coefficients with Gromacs.☆25Updated 7 months ago
- Temperature generator for Replica Exchange MD simulations☆25Updated last year
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆34Updated last year
- McDock: Simple Monte Carlo docking algorithm in C++☆10Updated 7 years ago
- ☆12Updated 9 months ago
- Using supervised machine learning to build collective variables for accelerated sampling☆27Updated 6 years ago
- Main code repository for the PLUMED-GUI plugin for VMD☆15Updated 2 years ago
- Compare optimized geometries and energies from various force fields with respect to a QM reference.☆13Updated 3 years ago
- Tools, tutorials, and wiki for GROMACS☆18Updated 4 years ago
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆11Updated 5 years ago
- The App Store for VMD extensions.☆11Updated last year
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆27Updated 7 months ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆40Updated 3 years ago
- Materials, issues and things for the 2018 Workshop and Hackathon☆14Updated 4 years ago
- PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems☆13Updated 2 years ago
- Quantum Mechanical Bespoke Force Field Derivation Toolkit☆12Updated 4 years ago
- Enhanced sampling methods for molecular dynamics simulations☆34Updated last year
- Different run and analysis scripts as described in the research guides.☆10Updated 2 years ago
- Utilities for molecular volume calculation☆10Updated 6 years ago
- Convenience functions for VMD-TCL scripting☆14Updated 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…☆17Updated 3 months ago