markusfleck / PARENTLinks
PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems
☆16Updated 4 years ago
Alternatives and similar repositories for PARENT
Users that are interested in PARENT are comparing it to the libraries listed below
Sorting:
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆40Updated 2 years ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆19Updated 2 years ago
- Temperature generator for Replica Exchange MD simulations☆29Updated 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
- Entropy from PDB conformational ensembles☆13Updated last year
- 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 8 months ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆34Updated 2 years ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆18Updated last week
- A tutorials suite for BioSimSpace.☆34Updated 3 months ago
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆43Updated 2 months ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Updated 2 years ago
- ☆25Updated 2 years ago
- Computation of the drug-target relative residence times from RAMD simulations☆21Updated last year
- Random Acceleration Molecular Dynamics in GROMACS☆43Updated last year
- 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
- A collections of scripts for working molecular dynamics simulations☆45Updated 6 months ago
- ☆43Updated last year
- ☆69Updated 2 years ago
- Tutorial using PLANTS (Protein-Ligand ANTSystem)☆12Updated 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
- ☆31Updated 2 weeks ago
- Some of useful tcl scripts to analyse data from VMD☆15Updated 3 years ago
- Python code for generating Boresch restraints from MD simulations☆22Updated 3 months ago
- Analysis of non-covalent interactions in MD trajectories☆66Updated last year
- ☆28Updated 2 years ago
- Q6 Repository -- EVB, FEP and LIE simulator.☆35Updated 2 years ago
- Examples of applications of pymbar to various problems in simulation and experiment☆23Updated 11 years ago
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆24Updated 6 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 last month
- Different run and analysis scripts as described in the research guides.☆13Updated 3 years ago