dkoes / md-scriptsLinks
A collections of scripts for working molecular dynamics simulations
☆45Updated 5 months ago
Alternatives and similar repositories for md-scripts
Users that are interested in md-scripts are comparing it to the libraries listed below
Sorting:
- ☆25Updated last year
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- ☆28Updated 8 months ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆46Updated 4 years ago
- Analysis of non-covalent interactions in MD trajectories☆65Updated last year
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆39Updated 2 years ago
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆60Updated 3 weeks ago
- Fully automated high-throughput MD pipeline☆86Updated last week
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated 2 years ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆34Updated 2 years ago
- Computational Chemistry Workflows☆56Updated 3 years ago
- Tool to predict water molecules placement and energy in ligand binding sites☆35Updated 3 months ago
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆34Updated last month
- This script makes a cyclic peptide or cyclic nucleotide topology file for GROMACS out of (specially prepared) linear molecule topology fi…☆14Updated 5 years ago
- ☆41Updated last year
- Collection of Python scripts to setup and run simulations with OpenMM☆17Updated 5 years ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆18Updated 3 months ago
- Cryptic pocket prediction using AlphaFold 2☆24Updated 3 years ago
- A tutorials suite for BioSimSpace.☆33Updated 2 months ago
- Implementation of Shape and Electrostatic similarity metric in deepFMPO.☆45Updated 3 years ago
- ☆39Updated 5 months ago
- Temperature generator for Replica Exchange MD simulations☆29Updated 3 years ago
- Set up relative free energy calculations using a common scaffold☆24Updated 4 months ago
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆72Updated 2 weeks ago
- MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshe…☆24Updated last year
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆19Updated 3 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
- Notebooks demonstrating how to do simple tasks related to free energy calculations.☆58Updated this week
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆21Updated 8 months ago
- Open Source, Automated free binding free energy calculation between protein and small molecule. An all-in-one workflow, free energy pertu…☆59Updated 8 months ago