callumjd / AMBER-Umbrella_COM_restraint_tutorialLinks
Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane
☆37Updated 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
Sorting:
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆49Updated 4 years ago
- Python code for generating Boresch restraints from MD simulations☆22Updated 3 years ago
- Examples of applications of pymbar to various problems in simulation and experiment☆23Updated 10 years ago
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆60Updated last year
- ☆65Updated last month
- A collections of scripts for working molecular dynamics simulations☆44Updated last month
- ☆39Updated last year
- PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems☆15Updated 3 years ago
- Analysis of non-covalent interactions in MD trajectories☆61Updated 8 months ago
- Set up relative free energy calculations using a common scaffold☆24Updated 3 weeks ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆72Updated 2 years ago
- Random Acceleration Molecular Dynamics in GROMACS☆39Updated last year
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆30Updated 3 years ago
- ☆30Updated 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
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆40Updated last week
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- ☆25Updated last year
- Temperature generator for Replica Exchange MD simulations☆29Updated 2 years ago
- Q6 Repository -- EVB, FEP and LIE simulator.☆34Updated last year
- Density based object completion over PBC.☆30Updated 9 months ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆18Updated 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.☆51Updated 5 months ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- ☆67Updated 2 years ago
- ☆28Updated 4 months ago
- Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface☆37Updated 3 years ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆83Updated 2 months ago
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆67Updated 2 years ago