Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane
☆41Aug 11, 2023Updated 2 years ago
Alternatives and similar repositories for AMBER-Umbrella_COM_restraint_tutorial
Users that are interested in AMBER-Umbrella_COM_restraint_tutorial are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Example files for Colvars module: https://github.com/Colvars/colvars☆13Dec 7, 2021Updated 4 years ago
- Adaptive string method implementation in AmberTools23 and Amber22☆14Jan 7, 2025Updated last year
- Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems☆15Jun 15, 2019Updated 6 years ago
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆24Oct 18, 2019Updated 6 years ago
- A Package for Parametrization of Molecular Mechanics Force Fields☆32Nov 13, 2022Updated 3 years ago
- Wordpress hosting with auto-scaling - Free Trial • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- A repository containing the build steps for the ccpbiosim workshop on QM/MM☆68Apr 3, 2026Updated last week
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆15Jan 3, 2026Updated 3 months ago
- ☆16Jul 28, 2022Updated 3 years ago
- Analysis of non-covalent interactions in MD trajectories☆68Jan 3, 2025Updated last year
- Examples of applications of pymbar to various problems in simulation and experiment☆23Jan 16, 2015Updated 11 years ago
- Spectral Gap Optimization of Parameters☆18Mar 28, 2020Updated 6 years ago
- A tutorials suite for BioSimSpace.☆36Oct 22, 2025Updated 5 months ago
- Generate Ramachandran plots for single PDB structure and as heatmap for MD trajectory☆11Apr 6, 2022Updated 4 years ago
- ☆33Sep 23, 2023Updated 2 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Data visualizations for biomolecular dynamics☆17Oct 30, 2018Updated 7 years ago
- Collection of tools for running MD, QM, and QM/MM calculations☆20Sep 27, 2025Updated 6 months ago
- Utilities to assist with Amber Molecular Dynamics structure preparation and MMPBSA.py energy methods☆20Oct 31, 2019Updated 6 years ago
- gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.☆302Dec 8, 2025Updated 4 months ago
- Repository of the data for PLUMED Masterclass 22.3☆14Jul 10, 2024Updated last year
- Real time monitoring and visualization of Amber MD simulations☆16Feb 6, 2020Updated 6 years ago
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆74Aug 11, 2023Updated 2 years ago
- Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.☆15Sep 20, 2018Updated 7 years ago
- A stripped-down set of just antechamber, sqm, and tleap.☆34Sep 20, 2021Updated 4 years ago
- Deploy open-source AI quickly and easily - Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- VMD Plugin and associated scripts to build lignin structures from topological specifications☆17Jul 17, 2025Updated 8 months ago
- This script makes a cyclic peptide or cyclic nucleotide topology file for GROMACS out of (specially prepared) linear molecule topology fi…☆15Nov 24, 2020Updated 5 years ago
- ParametrizANI - Fast, Accurate and Free Dihedral Parametrization in the Cloud with TorchANI☆22Jul 28, 2025Updated 8 months ago
- ☆25Aug 1, 2023Updated 2 years ago
- Plug-in for ChimeraX providing features for building and manipulating organic and organometallic molecules as well as displaying output f…☆34Mar 22, 2026Updated 3 weeks ago
- A python implementation of pdb2oniom for QM/MM (ONIOM) calculations☆11Oct 2, 2025Updated 6 months ago
- A collections of scripts for working molecular dynamics simulations☆45Feb 6, 2026Updated 2 months ago
- SAPT energy calculator built using MDAnalysis and Psi4☆15May 26, 2025Updated 10 months ago
- Python tutorial for estimating and clustering free energy landscapes with InfleCS.☆31May 6, 2022Updated 3 years ago
- Serverless GPU API endpoints on Runpod - Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Syntax highlighting for Orca input files in vim☆15Aug 29, 2022Updated 3 years ago
- A python implementation of the string method with swarms of trajectories using GROMACS☆19Oct 19, 2022Updated 3 years ago
- protein conformational spaces meet machine learning☆51Mar 26, 2026Updated 2 weeks ago
- Flexible Artificial Intelligence Docking☆18Aug 27, 2025Updated 7 months ago
- Biomolecular simulation trajectory/data analysis.☆164Updated this week
- The Beginner's Guide to Digital Chemistry☆18Nov 3, 2025Updated 5 months ago
- pyProCT is an open source cluster analysis software especially adapted for jobs related with structural proteomics. Its approach allows u…☆10Aug 24, 2017Updated 8 years ago