pamellaccar / gromacs_plumed_hremd
A step-by-step tutorial to run Molecular Dynamics Simulations with enhanced sampling of a pepitide using PLUMED implemented in GROMACS to perform replica exchanges
☆13Updated 8 months ago
Related projects ⓘ
Alternatives and complementary repositories for gromacs_plumed_hremd
- ☆25Updated last year
- Pras Server is a library to repair PDB or mmCIF structures, add missing heavy atoms and hydrogen atoms and assign secondary structure by …☆25Updated 4 months ago
- A Python program for QM/MM Simulations based on the Perturbed Matrix Method☆24Updated last year
- PyMOL-wasm port's binary and html/javascript code☆17Updated last year
- ☆25Updated last year
- ☆39Updated last year
- ☆32Updated 2 months ago
- An implementation of the 3SPN2 and 3SPN2.C coarse-grained DNA forcefields in OpenMM☆18Updated 6 months ago
- An implementation of the AWSEM coarse-grained protein folding forcefield in OpenMM☆35Updated 3 months ago
- Lab policies, training, style guides, etc.☆35Updated 7 months ago
- Some notes (cookbook) for pyMol. Protein Crystallography course.☆15Updated 3 years ago
- pKa estimates for proteins using an ensemble approach☆27Updated last month
- ☆32Updated 3 months ago
- An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics☆15Updated 2 years ago
- This repo contains the collection of codes to find designer interfacial mutations☆16Updated last year
- An open-source library for the analysis of protein interactions.☆29Updated 2 years ago
- Repo for the publication titled: "Key Interaction Networks: Identifying Evolutionarily Conserved Non-Covalent Interaction Networks Across…☆12Updated last year
- ☆18Updated 6 months ago
- Analyse Nucleic Acids Structure and Simulations with baRNAba☆41Updated 8 months ago
- model builder for molecular dynamics simulations☆13Updated last year
- Trusted force field files for gromacs☆40Updated 3 weeks ago
- We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU appr…☆15Updated 4 months ago
- Analysis of non-covalent interactions in MD trajectories☆51Updated last year
- development repository for PyInteraph2☆21Updated last year
- Collection of Python scripts to setup and run simulations with OpenMM☆14Updated 4 years ago
- Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over pop…☆50Updated 3 weeks ago
- Building and analyzing residue interaction networks with cofactors (includes tutorial).☆17Updated 3 years ago
- Automated construction of protein chimeras and their analysis.☆15Updated last year
- KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.☆23Updated 5 months ago
- ☆37Updated 3 months ago