leelasd / ligpargenLinks
A repository for tutorials and FAQ's about LigParGen
☆23Updated 7 years ago
Alternatives and similar repositories for ligpargen
Users that are interested in ligpargen are comparing it to the libraries listed below
Sorting:
- GridMAT-MD membrane analysis program☆25Updated 7 years ago
- Generate coarse-grained molecular dynamics models from atomistic trajectories.☆64Updated 2 years ago
- scripts for analyzing molecular dynamics trajectories using VMD☆39Updated 10 years ago
- ☆75Updated 10 months ago
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆34Updated 4 months ago
- The pDynamo molecular modeling and simulation program☆41Updated 4 months ago
- Challenge details, inputs, and (eventually) results for the SAMPL8 series of challenges☆25Updated 5 months ago
- Database of hand-built OPLS-AA parameters and topologies for 464 molecules. Zip files contains parameter and topologies for OpenMM, Groma…☆35Updated 7 years ago
- Physical validation of molecular simulations☆57Updated last month
- Q6 Repository -- EVB, FEP and LIE simulator.☆34Updated 2 years ago
- Calculation of water/solvent partition coefficients with Gromacs.☆28Updated last year
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆29Updated last year
- RESP with inter- and intra-molecular constraints in Psi4.☆32Updated 2 years ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆72Updated 2 years ago
- A general small molecule force field descended from AMBER99 and parm@Frosst, available in the SMIRNOFF format☆30Updated last year
- Set up relative free energy calculations using a common scaffold☆24Updated 2 months ago
- Automatic MARTINI parametrization of small organic molecules☆69Updated 5 months ago
- A fast solver for large scale MBAR/UWHAM equations☆40Updated last year
- Martini 3 small molecule database☆66Updated last month
- A python class for building a ZMatrix from a RDKit molecule. We can also do coordinate transformations between ZMatrix and Cartesian spac…☆15Updated 2 years ago
- 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
- OpenMM plugin to interface with PLUMED☆69Updated 8 months ago
- A python implementation of the string method with swarms of trajectories using GROMACS☆18Updated 3 years ago
- Examples of applications of pymbar to various problems in simulation and experiment☆23Updated 10 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
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆61Updated last year
- Best Practices article intended for LiveCoMS☆42Updated 5 years ago
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆70Updated last week
- Enhanced sampling methods for molecular dynamics simulations☆41Updated 2 years ago
- In-house tools for setting up arbitrary solute-solvent mixtures for simulation in GROMACS, Amber, OpenMM or other codes☆33Updated 5 years ago