MDAnalysis / UserGuide
User Guide for MDAnalysis
☆25Updated this week
Alternatives and similar repositories for UserGuide:
Users that are interested in UserGuide are comparing it to the libraries listed below
- Advanced toolkit for binding free energy calculations☆32Updated 2 months ago
- Temperature generator for Replica Exchange MD simulations☆27Updated 2 years ago
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆24Updated 4 years ago
- Q6 Repository -- EVB, FEP and LIE simulator.☆31Updated last year
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆31Updated last year
- Set up relative free energy calculations using a common scaffold☆22Updated 7 months ago
- A tool for setting up free energy simulations.☆35Updated 2 years ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆18Updated 2 years ago
- Analysis of non-covalent interactions in MD trajectories☆55Updated 3 months ago
- ☆33Updated 6 months ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆31Updated 5 years ago
- Density based object completion over PBC.☆27Updated 3 months ago
- RESP with inter- and intra-molecular constraints in Psi4.☆30Updated last year
- A command line application to launch molecular dynamics simulations with OpenMM☆40Updated 2 years ago
- Python code for generating Boresch restraints from MD simulations☆20Updated 2 years ago
- Random Acceleration Molecular Dynamics in GROMACS☆36Updated 8 months ago
- The MDAnalysis Toolkits Registry☆17Updated last week
- Different run and analysis scripts as described in the research guides.☆13Updated 2 years ago
- The peleffy (PELE Force Field Yielder) is a Python package that builds PELE-compatible force field templates.☆12Updated last week
- ☆26Updated 2 weeks ago
- ☆26Updated last year
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆31Updated this week
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Updated last year
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆44Updated 4 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
- A tutorials suite for BioSimSpace.☆24Updated last month
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆58Updated last year
- Workshop - Analysis of Molecular Dynamics Simulation Using Python☆17Updated 4 years ago