markovmodel / pytramLinks
The pytram package is deprecated and no longer supported. We recommend to switch to PyEMMA
☆9Updated 9 years ago
Alternatives and similar repositories for pytram
Users that are interested in pytram are comparing it to the libraries listed below
Sorting:
- Bayesian tools for fitting molecular mechanics torsion parameters to quantum chemical data.☆21Updated 3 years ago
- Basis sets, estimators and solvers for the variational approach of conformation dynamics. NOTE: the code has been merged with PyEMMA and …☆10Updated 8 years ago
- Winter is coming...☆12Updated 6 years ago
- An example of how to write a plugin for OpenMM☆31Updated last year
- A python framework to run adaptive Markov state model (MSM) simulation on HPC resources☆18Updated last year
- How to analyze molecular dynamics data with PyEMMA☆76Updated 6 years ago
- Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations☆20Updated 7 years ago
- Get access to our MD data files.☆29Updated last year
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆43Updated 3 years ago
- Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling☆33Updated this week
- Python bindings for TNG file format☆13Updated 7 months ago
- Tools for estimating and analyzing Markov state models☆42Updated 2 years ago
- Package for consistent reporting of relative free energy results☆39Updated last week
- MDToolbox: A MATLAB/Octave toolbox for statistical analysis of molecular dynamics trajectories☆25Updated 5 years ago
- Generate coarse-grained molecular dynamics models from atomistic trajectories.☆64Updated 2 years ago
- Set up relative free energy calculations using a common scaffold☆24Updated 2 months ago
- Main code repository for FATSLiM☆21Updated 3 years ago
- A command line application to launch molecular dynamics simulations with OpenMM☆40Updated 3 years ago
- Ensembler is a python package that provides fast and easy access to 1D and 2D model system simulations. It can be used for method develop…☆53Updated last year
- Calculation of water/solvent partition coefficients with Gromacs.☆28Updated 8 months ago
- Best practice document for alchemical free energy calculations going to livecoms journal☆74Updated 2 weeks ago
- Compare optimized geometries and energies from various force fields with respect to a QM reference.☆13Updated 4 years ago
- Dihedral scanner with wavefront propagation☆34Updated last month
- For discussing and aggregating data for force field development☆15Updated 8 years ago
- Q6 Repository -- EVB, FEP and LIE simulator.☆31Updated last year
- Encoding of transition probabilities with undirected graphical models☆9Updated 6 years ago
- OpenMM plugin to interface with PLUMED☆66Updated 3 months ago
- Physical validation of molecular simulations☆56Updated 2 months ago
- Enhanced sampling methods for molecular dynamics simulations☆37Updated 2 years ago
- A general small molecule force field descended from AMBER99 and parm@Frosst, available in the SMIRNOFF format☆29Updated 9 months ago