dkoes / md-scriptsLinks
A collections of scripts for working molecular dynamics simulations
☆44Updated last month
Alternatives and similar repositories for md-scripts
Users that are interested in md-scripts are comparing it to the libraries listed below
Sorting:
- ☆28Updated 4 months ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆37Updated 2 years ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated 3 weeks ago
- ☆25Updated last year
- Analysis of non-covalent interactions in MD trajectories☆61Updated 8 months ago
- Collection of Python scripts to setup and run simulations with OpenMM☆17Updated 5 years ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆45Updated 4 years ago
- Computational Chemistry Workflows☆55Updated 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 2 years ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆32Updated this week
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated 2 years ago
- Different run and analysis scripts as described in the research guides.☆13Updated 3 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.☆50Updated 5 months ago
- Random Acceleration Molecular Dynamics in GROMACS☆39Updated last year
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆19Updated 2 years ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆30Updated 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
- Set up relative free energy calculations using a common scaffold☆24Updated 3 weeks ago
- Free Parametrization for Small Molecules☆36Updated 2 weeks ago
- A tutorials suite for BioSimSpace.☆26Updated 4 months ago
- Temperature generator for Replica Exchange MD simulations☆29Updated 2 years ago
- ☆27Updated 4 years ago
- ☆65Updated last month
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆32Updated 3 months ago
- ☆44Updated 3 years ago
- Accurate prediction of protein pKa with representation learning☆43Updated 7 months ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆83Updated last month
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆17Updated last week