Search Results for "amber"
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Showing 36 open source projects for "amber"
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Algernon
Small self-contained pure-Go web server with Lua, Markdown, HTTP/2
Web server with built-in support for QUIC, HTTP/2, Lua, Teal, Markdown, Pongo2, HyperApp, Amber, Sass(SCSS), GCSS, JSX, BoltDB (built-in, stores the database in a file, like SQLite), Redis, PostgreSQL, MariaDB/MySQL, rate limiting, graceful shutdown, plugins, users and permissions. Written in Go. Uses Bolt (built-in), MySQL, PostgreSQL or Redis (recommended) for the database backend, permissions2 for handling users and permissions, gopher-Lua for interpreting and running Lua, optional Teal for type-safe Lua scripting, http2 for serving HTTP/2, QUIC for serving over QUIC, blackfriday for Markdown rendering, amber for Amber templates, Pongo2 for Pongo2 templates, Sass(SCSS) and GCSS for CSS preprocessing. logrus is used for logging, goja-babel for converting from JSX to JavaScript, tollbooth for rate limiting, pie for plugins and graceful for graceful shutdowns. -
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CoreAmber is a Arm Processor structure 32 Bit comes from Amber processor the code is been written in CX & Verilog
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amber
A Crystal web framework that makes building applications fast
Amber makes building web applications fast, simple, and enjoyable. Get started with blazing-fast performance. Amber provides the bare metal performance of the Crystal Language. It provides productivity and happiness through a powerful CLI and familiar design patterns seen in Kemal, Rails, Phoenix and other popular frameworks. Use code generation and scaffolding features to rapidly build prototypes. -
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ERmod
Approximate solvation free energy calculator
...The program allows users to calculate the solvation free energy to arbitrary solvents, including inhomogeneous systems, and can run in cooperation with state-of-art molecular simulation software, such as LAMMPS, GROMACS and/or AMBER. -
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slop-index
Analyzer that spots AI-slop and boilerplate in text and webpages
Slop Index is a quality scanner for modern content. It detects the tell-tale patterns of “AI slop” and SEO filler—repetitive phrasing, template intros, hedging, buzzword stuffing, outline-shaped paragraphs, and other signals that make writing feel generic. Paste text, point it at a URL, or batch a whole sitemap; Slop Index returns a 0–100 Slop Score with a transparent breakdown and a de-slop checklist you can act on immediately. Under the hood, Slop Index blends classical NLP with... -
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SmartRulerCapture
Professional screen capture tool with built‑in rulers multi-capture
Smart Ruler Capture is a professional screen capture tool designed for designers, developers, and anyone needing precise on‑screen measurements. It features multiple active capture zones, an overlay ruler with configurable units (px, in, cm), and a customizable grid for perfect alignment. The app offers eight color themes, full keyboard control, and works entirely offline - no analytics, no cloud uploads. Settings are automatically saved between sessions. Includes handy keyboard shortcuts... -
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InventraX
desktop application for tracking inventory and physical assets.
InventraX is a desktop application for tracking inventory and physical assets. It runs fully offline, stores all data in a local SQLite database, and exports to Excel, CSV, and PDF. -
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D2X-XL
OpenGL port of the classic 6dof 3D shooter Descent
D2X-XL is an OpenGL port of the classic 3D Shooter game Descent 2 for Win32, Linux and Mac OS X, containing many enhancements and bug fixes while preserving full backwards compatibility. -
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Gabedit is a Graphical User Interface for FireFly (PC-Gamess), Gamess-US, Gaussian, Molcas, Molpro, MPQC, NWChem, OpenMopac, Orca, PSI4 and Q-Chem computational chemistry packages.
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ForceGen
Derives force constants from Gaussian QM for Gromacs MD
...DOI: 10.1007/s00894-017-3530-6 Instruction video: https://youtu.be/fQVXv8Ge_tg This Java executable jar derives second order bond force constants for bond stretch and bond angle from quantum mechanical Gaussian calculations. The calculations are compatible with the Amber force field family or any force field derived from the second order tensor of the Hessian from molecular fragments. The output has been made compatible with the Gromacs topology format. Examples of use include the derivation of bond force constants and equilibrium values for: -bonded metals in protein active sites -modified amino acids -small molecules/drug molecules A zip of examples files can be found by following the "Browse All Files" link. ... -
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MolDynSim
TrajLab subproject: Molecular dynamics simulations in MATLAB
This is a subproject of TrajLab which is probably the first attempt for a general purpose molecular simulation package in MATLAB. While the authors are aware that many other highly specialized and highly optimized program packages for the same purpose exist (e. g. AMBER, GROMACS, NAMD, etc.), the MATLAB environment offers easy access to manipulating the codes, testing novel algorithms, non-standard force fields and performing all kinds of numerical experiments. To be used mainly in research and teaching! Started early 2010, MolDynSim is still in an early (alpha) stage, and any help in further development is highly appreciated. ... -
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MetaStable
TrajLab subproject: Metastability analysis of molecular conformations
This is a subproject of TrajLab which is probably the first attempt for a general purpose molecular simulation package in MATLAB. While the authors are aware that many other highly specialized and highly optimized program packages for the same purpose exist (e. g. AMBER, GROMACS, NAMD, etc.), the MATLAB environment offers easy access to manipulating the codes, testing novel algorithms, non-standard force fields and performing all kinds of numerical experiments. To be used mainly in research and teaching! Started early 2010, MetaStable is still in an early (alpha) stage, and any help in further development is highly appreciated. ... -
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AmberAnalysis
Command-line tools for analyzing Amber Molecular Dynamics simulations.
A suite of command-line tools for analyzing chemically relevant features of an Amber Molecular Dynamics simulation. Can detect the position of a planar interface between two substances and plot density relative to that interface for atoms of an arbitrary type, name, charge, or residue. Orientation of three-atom residues (such as water) may be calculated and plotted. Uses parallel processing to detect hydrogen bonds, and can produce a bonding profile. -
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Fragment-based Peptide Docking
Fragment-based Peptide Docking
A fortran based fragmentizing-docking-remerging program for long peptides (10-16 amino acids) docking simulations. This program is compiled by intel fortran at OpenSUSE 64-bits. Designed for 4GPU servers. NOTE: AMBER software packages, AMBER Tools and pmemd.cuda must be normally installed to fully operate this program. However you can still sample massive initial structures (500k~2m peptide conformations) without AMBER. Reference: http://pubs.rsc.org/en/content/articlelanding/2017/cp/c6cp07136h Supporter: JM Liao, tiomiya@hotmail.com -
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Amber Crux
Amber Crux is a 2D graphical adventure game.
Amber Crux is a graphical adventure game, set in a randomly generated fantasy world. The player will travel through a variety of different environments, such as forests, towns and dungeons, fighting against vicious monsters and collecting interesting artifacts in order to complete their quest. -
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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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DDPT
A Comprehensive Toolbox for the Analysis of Protein Motion
Toolbox allowing calculation of elastic network models and principle component analysis. It allows the analysis of pdb files or trajectories taken from; Gromacs, Amber, and DL POLY. As well as calculation of the normal modes it also allows comparison of the modes with experimental protein motion, variation of modes with mutation or ligand binding, and calculation of molecular dynamic entropies. -
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ASyncRE-BigJob
Asynchronous Replica Exchange with BigJob
A distributed replica exchange molecular dynamics framework written in Python built on top of BigJob (https://github.com/saga-project/BigJob/wiki). The software is extensible to any molecular dynamics engines. Modules for AMBER and IMPACT are included. Download: https://sourceforge.net/projects/asyncrebigjob/files/latest/download See README for installation instructions. See documentation in doc/ subdirectory. Git access: git clone https://github.com/saga-project/asyncre-bigjob -
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TrajLab
MATLAB based programs for trajectory simulations of molecules
...Note that each of the two sub-projects has its own SVN repository, wiki, tracker, etc: Probably TrajLab is the first attempt for a general purpose molecular simulation package in MATLAB. While the authors are aware that many other highly specialized and highly optimized program packages for the same purpose exist (e. g. AMBER, GROMACS, NAMD, etc.), the MATLAB environment offers easy access to manipulating the codes, testing novel algorithms, non-standard force fields and performing all kinds of numerical experiments. To be used mainly in teaching! -
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