Search Results for "md"
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Showing 18 open source projects for "md"
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BioEmu
Inference code for scalable emulation of protein equilibrium ensembles
...To reconstruct the side-chains, several tools are available. As an example, we interface with HPacker to conduct side-chain reconstruction and also provide basic tooling for running a short molecular dynamics (MD) equilibration. -
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DB-GPT
Revolutionizing Database Interactions with Private LLM Technology
DB-GPT is an experimental open-source project that uses localized GPT large models to interact with your data and environment. With this solution, you can be assured that there is no risk of data leakage, and your data is 100% private and secure. -
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Jupytext
Jupyter Notebooks as Markdown Documents, Julia, Python or R scripts
...Text notebooks are well suited for version control. You can also edit or refactor them in an IDE - the .py notebook above is a regular Python file. Text notebooks with a .py or .md extension are well suited for version control. They can be edited or authored conveniently in an IDE. You can open and run them as notebooks in Jupyter Lab with a right click. However, the notebook outputs are lost when the notebook is closed, as only the notebook inputs are saved in text notebooks. -
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dirsearch
Web path scanner
An advanced command-line tool designed to brute force directories and files in webservers, AKA web path scanner. Wordlist is a text file, each line is a path. About extensions, unlike other tools, dirsearch only replaces the %EXT% keyword with extensions from -e flag. For wordlists without %EXT% (like SecLists), -f | --force-extensions switch is required to append extensions to every word in wordlist, as well as the /. To use multiple wordlists, you can separate your wordlists with commas.... -
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FairChem
FAIR Chemistry's library of machine learning methods for chemistry
FAIRChem is a unified library for machine learning in chemistry and materials, consolidating data, pretrained models, demos, and application code into a single, versioned toolkit. Version 2 modernizes the stack with a cleaner core package and breaking changes relative to V1, focusing on simpler installs and a stable API surface for production and research. The centerpiece models (e.g., UMA variants) plug directly into the ASE ecosystem via a FAIRChem calculator, so users can run relaxations,... -
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GromacsProSuite
Graphical User Interface for Gromacs
...Beyond simulation execution, it includes advanced trajectory processing and analysis tools such as RMSD, RMSF, SASA, clustering, PCA, hydrogen-bond analysis, Ramachandran plots, and FEL mapping. With integrated visualization and plotting utilities, it offers a unified platform for researchers, educators, and students to perform complete MD workflows efficiently and reproducibly. Our Goal is to bring MD simulations to every biologist's toolkit. -
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SDF Merger
Desktop application for merging multiple SDF files into a single SDF
...Real-time Progress Tracking: Visual progress bar and status updates during merging Technical Specifications: 1. Language: Python 3 2. GUI Framework: Tkinter 3. Chemistry Library: RDKit for chemical data processing 4. File Formats: Input/Output in SDF format Citation Md. Ismiel Hossen, A. (2026). SDF Merger: A Desktop and Web Tool for Merging Chemical Structure Data Files (v1.1). Zenodo. https://doi.org/10.5281/zenodo.18291398 -
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CAMPARI
Software for molecular simulations and trajectory analysis
We are proud to introduce version 5 of CAMPARI. We have added a number of new features, most notably a Python interface for interpreting user-supplied code (with the help of ForPy), a novel trajectory storage standard (with the help of libpqxx/PostgreSQL), and a module for performing transition path theory. Naturally, CAMPARI continues to provide the reference implementation of the ABSINTH force field paradigm and implicit solvation model. CAMPARI is a joint package for performing and... -
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Linkchecker for Markdown
Python asyncio + aiohttp Markdown *.md URL link checker
Blazing-fast (10000 Markdown files per second) Python asyncio / aiohttp based simple check of links in Markdown .md files only. This tool is very helpful for large Markdown-based Jekyll and Hugo sites as well as Markdown-based MkDocs documentation projects. It is very fast and simple. -
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Molecular Dynamics Studio
Molecular Dynamics Cell Construction
...NanoEngineer-1 is a molecular CAD software written by Nanorex and provides the user an easy way to create molecules, while the software modifications allow the user to type atoms using multiple force fields. PACKMOL can generate a random collection of molecules using the molecule templates from NanoEngineer-1 thus providing the initial MD cell. Modifications to PACKMOL allow the atom type data to be passed through to the MSI2LMP software. MSI2LMP creates a LAMMPS input file based on class I or class II force fields. MSI2LMP was modified to use numerically coded force field data generated by NanoEngineer-1. The MMP file format was extended and integrated into all three software applications. ... -
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System Storage Manager
A single tool to manage your storage
System Storage Manager provides easy to use command line interface to manage your storage using various technologies like lvm, btrfs, encrypted volumes and possibly more. In more sophisticated enterprise storage environments, management with Device Mapper (dm), Logical Volume Manager (LVM), or Multiple Devices (md) is becoming increasingly more difficult. With file systems added to the mix, the number of tools needed to configure and manage storage has grown so large that it is simply not user friendly. With so many options for a system administrator to consider, the opportunity for errors and problems is large. The btrfs administration tools have shown us that storage management can be simplified, and we are working to bring that ease of use to Linux filesystems in general. -
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ProtPOS
Prediction of PROTtein Preferred Orientation on a Surface
...It searches quickly for the low energy protein poses in all translational and rotational degrees of freedom of the protein with respect to the surface using particle swarm optimization. Each successful run returns the lowest energy orientation of the protein on the surface in PDB format, which is readily used for MD simulations. ProtPOS is implemented in Python, making use of the PyMOL library for generating protein conformations and calling GROMACS externally to calculate protein-surface interaction energies. https://cbbio.online/software/protpos/ -
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PyBrella
Python script to automate umbrella sampling with AMBER
PyBrella is a script designed to automate the umbrella sampling process, using the AMBER molecular dynamics package. -
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MDcons(Molecular Dynamics consensus)
Interpretation of Biomolecular MD simulations
MDcons is a tool to analyze conserved contacts during Molecular Dynamics (MD) simulations of Protein, Rna, Dna & Ligand based complexes. The input is either a Molecular Dynamics trajectory or a set of snapshots. The input can also be a single snapshot. The outputs are (1) map of most/less frequently conserved contacts during MD (2) a list of most/less frequently conserved contacts during MD. -
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Use SASSIE to generate and manipulate large numbers of molecular structures and then calculate the SAXS, SANS, and neutron reflectivity profiles from atomistic structures. Use for intrinsically disordered proteins. We need alpha-testers and developers.
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init4boot provides iSCSI boot for Xen dom0 and domU, kvm guests and bare metal systems - currently for Debian, Ubuntu and Fedora. It's an extensible tool set for creating initramfs with support for: iSCSI, lvm2, md, multipath, network, tftp config,
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Markdown wysiwyg - A web based wysiwyg editor for John Gruber's Markdown. This allows a gentle introduction to Markdown for novices. Works with Mozilla and IE. Not yet tested with safari or konqueror.
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