Eigenstate / psfgen
NAMD's psfgen + Python improvements
☆13Updated 4 months ago
Alternatives and similar repositories for psfgen:
Users that are interested in psfgen are comparing it to the libraries listed below
- We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU appr…☆15Updated 6 months ago
- A command line application to launch molecular dynamics simulations with OpenMM☆39Updated 2 years ago
- pKa estimates for proteins using an ensemble approach☆27Updated 3 months ago
- Build conformational representations of Intrinsically Disordered Proteins and Regions by a guided sampling of the protein torsion space☆21Updated this week
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆28Updated 4 years ago
- A Machine Learned Molecular Mechanics Force Field with integration into GROMACS and OpenMM☆35Updated 2 weeks ago
- Standalone charge assignment from Espaloma framework.☆38Updated 6 months ago
- Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems☆14Updated 5 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…☆51Updated 8 months ago
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆28Updated 11 months ago
- Sire Molecular Simulations Framework☆46Updated this week
- ☆33Updated 4 months ago
- Package for consistent reporting of relative free energy results☆37Updated last week
- RESP with inter- and intra-molecular constraints in Psi4.☆29Updated last year
- TSCoDe is a systematical conformational embedder for small molecules. It helps computational chemists build transition states and binding…☆12Updated last week
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆24Updated 4 years ago
- Conformer-Rotamer Ensemble Sampling Tool based on the xtb Semiempirical Extended Tight-Binding Program Package☆29Updated this week
- The OpenMM Cookbook and Tutorials☆39Updated last year
- Analysis of non-covalent interactions in MD trajectories☆51Updated 2 weeks ago
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆27Updated 2 months ago
- A simple implementation of replica exchange MD simulations for OpenMM.☆23Updated 3 years ago
- Repository for Chemical Perception Sampling Tools☆19Updated 5 months ago
- ☆25Updated last year
- LAST: Latent Space Assisted Adaptive Sampling for Protein Trajectories☆11Updated 2 years ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆22Updated last month
- Given an RDKit molecule that does not sanitise, correct it until it does☆36Updated 9 months ago
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆21Updated 5 years ago
- GaudiMM: A modular optimization platform for molecular design☆32Updated 8 months ago
- Unified Free Energy Dynamics (UFED) simulations with OpenMM☆26Updated 10 months ago
- Partial Charge assignment for Molecular Dynamics☆17Updated 5 months ago