markusfleck / PARENTLinks
PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems
☆16Updated 3 years ago
Alternatives and similar repositories for PARENT
Users that are interested in PARENT are comparing it to the libraries listed below
Sorting:
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆39Updated 2 years ago
- Temperature generator for Replica Exchange MD simulations☆29Updated 3 years ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆49Updated 4 years ago
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆24Updated 6 years ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆18Updated 2 years ago
- Tutorial using PLANTS (Protein-Ligand ANTSystem)☆12Updated last year
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆18Updated 3 months ago
- ☆40Updated last year
- Entropy from PDB conformational ensembles☆11Updated last year
- A collections of scripts for working molecular dynamics simulations☆45Updated 5 months ago
- Random Acceleration Molecular Dynamics in GROMACS☆42Updated last year
- Repository of the data for PLUMED Masterclass 22.3☆14Updated last year
- A tutorials suite for BioSimSpace.☆33Updated 2 months ago
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆42Updated last month
- Different run and analysis scripts as described in the research guides.☆13Updated 3 years ago
- ☆28Updated 2 years ago
- ☆40Updated last year
- Automatic Martini force field generator for small organic molecules (up to 25 heavy atoms), Martini 3 compatible☆31Updated 2 weeks ago
- ☆25Updated last year
- Analysis of non-covalent interactions in MD trajectories☆65Updated last year
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆34Updated 2 years ago
- ☆69Updated 2 years ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆89Updated 5 months ago
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆72Updated last week
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆70Updated 2 years ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆30Updated 4 years ago
- Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface☆41Updated 4 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated 2 years ago
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆15Updated last week
- MDANCE: O(N) clustering for molecular dynamics. Process 1.5M frames in 40min. 8 specialized algorithms.☆97Updated last month