drroe / AmberMdPrepLinks
Wrapper script for preparing explicitly solvated systems for molecular dynamics simulations with Amber.
☆17Updated last year
Alternatives and similar repositories for AmberMdPrep
Users that are interested in AmberMdPrep are comparing it to the libraries listed below
Sorting:
- Analysis of non-covalent interactions in MD trajectories☆62Updated 8 months ago
- ☆53Updated 3 months ago
- ☆65Updated 2 months ago
- A collections of scripts for working molecular dynamics simulations☆44Updated last month
- MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshe…☆23Updated last year
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated 2 years ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆84Updated 2 months ago
- ☆39Updated last year
- Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over pop…☆60Updated last week
- ☆28Updated 4 months ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆49Updated 4 years 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
- Q6 Repository -- EVB, FEP and LIE simulator.☆34Updated last year
- Collection of Python scripts to setup and run simulations with OpenMM☆17Updated 5 years ago
- Accurate prediction of protein pKa with representation learning☆43Updated 7 months ago
- Stable version of MCCE.☆10Updated last month
- Set up relative free energy calculations using a common scaffold☆24Updated last month
- Random Acceleration Molecular Dynamics in GROMACS☆39Updated last year
- ☆56Updated 2 years ago
- Utilities to assist with Amber Molecular Dynamics structure preparation and MMPBSA.py energy methods☆19Updated 5 years ago
- Density based object completion over PBC.☆30Updated 9 months ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆45Updated 4 years ago
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆19Updated 2 years ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆65Updated 4 years ago
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆29Updated last year
- PyRod - Tracing water molecules in molecular dynamics simulations☆50Updated 4 years ago
- A python toolkit for analysing membrane protein-lipid interactions.☆68Updated 2 years ago
- Alchemical mutation scoring map☆40Updated last week
- Trusted force field files for gromacs☆59Updated 10 months ago
- mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data☆35Updated last week