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by Omnia Molecular Dynamics (Organization)
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Packages
| Name | Latest Version | Summary | Updated | License |
|---|
| modeller | 9.20 | Comparative modeling by satisfaction of spatial restraints | Mar 25, 2025 | Free for academic use |
| openmm | 7.4.2 | A high performance toolkit for molecular simulation. | Mar 25, 2025 | LGPL and MIT |
| fftw3f | 3.3.4 | The fastest Fourier transform in the west. | Mar 25, 2025 | GPL |
| mdtraj | 1.9.1 | A modern, open library for the analysis of molecular dynamics trajectories | Mar 25, 2025 | GNU Lesser General Public License v2 or later (LGPLv2+) |
| parmed | 3.2.0 | A package for parsing, interconverting, manipulating, and simulating biomolecular simulations with many packages | Mar 25, 2025 | LGPL |
| openmmtools | 0.20.0 | An OpenMM toolkit: test systems, integrators, and alchemical support | Mar 25, 2025 | MIT |
| pdbfixer | 1.6 | PDBFixer fixes problems in PDB files to prepare them for molecular simulation. | Mar 25, 2025 | MIT |
| packmol | 2016.06.09 | Packing Optimization for Molecular Dynamics Simulations | Mar 25, 2025 | GPL |
| ambermini | 16.16.0 | A stripped-down set of just antechamber, sqm, and tleap. See https://github.com/swails/ambermini | Mar 25, 2025 | GNU GPL v3 |
| shiftx2 | 1.10 | SHIFTX2 predicts both the backbone and side chain 1H, 13C and 15N chemical shifts for proteins using their structural (PDB) coordinates as input. | Mar 25, 2025 | All rights reserved |
| openmoltools | 0.8.7 | — | Mar 25, 2025 | MIT License |
| openforcefield | 0.8.4 | — | Mar 25, 2025 | MIT |
| termcolor | 1.1.0 | ANSII Color formatting for output in terminal. | Mar 25, 2025 | MIT License |
| msmtools | 1.2.1 | Tools for estimating and analyzing Markov state models | Mar 25, 2025 | LGPL-3 |
| openforcefields | 2.0.0rc.2 | Force fields released by the Open Force Field Initiative | Mar 25, 2025 | CC-BY |
| nose-timer | 0.5.0 | A timer plugin for nosetests | Mar 25, 2025 | MIT License or BSD License |
| pyemma | 2.4 | PyEMMA (EMMA = Emma's Markov Model Algorithms) is an open source Python/C package for analysis of extensive molecular dynamics simulations | Mar 25, 2025 | LGPLv3+ |
| smirnoff99frosst | 1.1.0 | The smirnoff99Frosst line of force fields | Mar 25, 2025 | CC-BY |
| thermotools | 0.2.6 | Lowlevel implementation toolbox for the analyis of multi-ensemble calculations | Mar 25, 2025 | GNU Lesser Public License v3+ |
| bhmm | 0.6.1 | Bayesian hidden Markov models for analysis of single-molecule trajectory data | Mar 25, 2025 | GNU Lesser General Public License v3 or later (LGPLv3+) |
| pymbar | 3.0.3 | Python implementation of the multistate Bennett acceptance ratio (MBAR) method. | Mar 25, 2025 | MIT |
| yank | 0.25.2 | — | Mar 25, 2025 | MIT |
| msmbuilder | 3.8.0 | MSMBuilder: Statistical models for biomolecular dynamics | Mar 25, 2025 | LGPLv2.1+ |
| scripttest | 1.3 | scripttest is a library to help you test your interactive command-line applications. | Mar 25, 2025 | — |
| clusterutils | 0.3.1 | Tools for use in compute cluster environments. | Mar 25, 2025 | GNU Lesser General Public License v2 or later (LGPLv2+) |