limresgrp / FMAP_v1
Codes to use funnel-metadynamics and funnel metadynamics automated protocol
☆27Updated 2 years ago
Related projects ⓘ
Alternatives and complementary repositories for FMAP_v1
- ☆25Updated 10 months ago
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆13Updated last year
- Set up relative free energy calculations using a common scaffold☆22Updated 3 months ago
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆12Updated 3 months ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated 11 months ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆34Updated last year
- Computational Chemistry Workflows☆53Updated 2 years ago
- ☆26Updated 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…☆30Updated 9 months ago
- Random Acceleration Molecular Dynamics in GROMACS☆32Updated 4 months ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆15Updated 2 weeks ago
- Python code for generating Boresch restraints from MD simulations☆18Updated 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.☆43Updated 2 weeks ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆22Updated this week
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- An OpenMM plugin that implements the Alchemical Transfer Potential☆37Updated last year
- ☆18Updated 3 years ago
- A collections of scripts for working molecular dynamics simulations☆40Updated 5 months ago
- Different run and analysis scripts as described in the research guides.☆10Updated 2 years ago
- ☆25Updated last year
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆41Updated 3 years ago
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆17Updated 2 years ago
- ☆29Updated last month
- ☆27Updated 5 months ago
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆10Updated 2 years ago
- Automate MD associated calculations☆35Updated this week
- ☆39Updated 4 months ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆70Updated 5 months ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆43Updated 3 years ago
- Tool to predict water molecules placement and energy in ligand binding sites☆27Updated 4 months ago