cameronabrams / psfgen
TcL/VMD/psfgen/bash scripts for generating MD systems for use with NAMD
☆9Updated last year
Alternatives and similar repositories for psfgen:
Users that are interested in psfgen are comparing it to the libraries listed below
- Physical validation of molecular simulations☆56Updated last month
- ☆10Updated 5 years ago
- fast functionalisation of molecules☆36Updated 3 years ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- Package for consistent reporting of relative free energy results☆39Updated last week
- core data models of the Open Free Energy ecosystem☆35Updated last week
- 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
- Collection of interaction and molecule parameters for the Martini3 force-field☆14Updated 2 years ago
- Solvation Structure and Thermodynamic Mapping☆39Updated last year
- ☆15Updated 3 years ago
- A simple implementation of replica exchange MD simulations for OpenMM.☆23Updated 3 years ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆24Updated 5 months ago
- QM-based enzyme model generation and validation.☆12Updated 8 months ago
- Command line interface for MDAnalysis☆20Updated 10 months ago
- We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU appr…☆16Updated 10 months ago
- OpenMM plugin to interface with PLUMED☆66Updated 2 months ago
- ☆64Updated last year
- A machine learned Molecular Mechanics force field with integration into GROMACS and OpenMM☆39Updated last month
- Useful Collective Variables for OpenMM☆13Updated last year
- A comprehensive toolkit for predicting free energies☆52Updated 3 months ago
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆29Updated last year
- ☆10Updated last year
- Scripts to convert between PDB to Tinker XYZ files, without using the existing TINKER programs for conversion.☆14Updated 3 years ago
- mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data☆33Updated last month
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆67Updated last week
- TUPÃ was developed to analyze electric field properties in molecular simulations☆20Updated last year
- Sire Molecular Simulations Framework☆54Updated 2 weeks ago
- Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-…☆45Updated 8 months ago
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆43Updated 3 years ago
- This package contains tools for setting up hybrid-topology FE calculations☆28Updated this week