Search Results for "md" - Page 3
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Showing 111 open source projects for "md"
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SAMFF
A Refined Empirical Force Field to Model Protein-SAM Interactions
Understanding protein interaction with material surfaces is important for the development of nanotechnological devices. The structures and dynamics of proteins can be studied via molecular dynamics (MD) if the protein-surface interactions can be accurately modeled. Based on AMBER14 and GAFF, we systematically tuned the Lennard-Jones parameters of selected amino acid sidechains and the functional group of SAM with repeated metadynamics and umbrella sampling simulations. The final parameter set has yielded a significant improvement in the free energy values with R = 0.83 and MSE = 0.65 kcal/mol. ... -
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usb-md
modified Linux USB driver kernel module
modified USB driver for teaching purpose -
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ForceGen
Derives force constants from Gaussian QM for Gromacs MD
Please cite: ForceGen: atomic covalent bond constant derivation for Gromacs. Nash A, Collier T, Birch HL, de Leeuw NH. Journal of Molecular Modeling (2018), (24)5. 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... -
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OpenGrowth
OpenGrowth is a program which constructs de novo ligands for proteins.
...OpenGrowthGUI, FOG2.0, and the 3Mer-Screen stand-alone can be found in OpenGrowth_1.0.zip. To prepare new fragments you need BuildingFragments_1.0.1.zip and the scripts for MD simulations are in MD-Scripts_1.0.1.zip. SMoG2016.tar.gz allows to compute a score with the newly developed function (J. Chem. Inf. Mod., http://pubs.acs.org/doi/abs/10.1021/acs.jcim.6b00610). For any questions, please send emails exclusively at opengrowth-discuss@lists.sourceforge.net. -
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dtime Decimal Time Library
Decimal time library for Linux/*nix
The dtime library is a project aimed at providing a set of decimal (metric) time replacement functions for the standard *nix time functions, allowing programmers to easily develop programs that work with decimal times. Decimal time systems divide the day into segments based on 10. Examples units are centidays (cd), millidays (md), and microdays (ud). -
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Iphigenie
A fast and versatile molecular dynamics program
The molecular mechanics (MM) program Iphigenie provides a broad range of molecular dynamics (MD) methods and technologies, including polarizable force fields (PMM), the HADES reaction field, and QM/(P)MM hybrid simulations. -
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Memory Dwell
NASA core Flight System Memory Dwell Application
OBSOLETE - Please proceed to new repo: https://github.com/nasa/MD This project will be closed in the near future The Memory Dwell application (MD) is a core Flight System (cFS) application that is a plug in to the Core Flight Executive (cFE) component of the cFS. The cFS is a platform and project independent reusable software framework and set of reusable applications developed by NASA Goddard Space Flight Center. -
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Limit Checker
NASA core Flight System Limit Checker Application
OBSOLETE - Please proceed to new repo: https://github.com/nasa/MD This project will be closed in the near future The Limit Checker application (LC) is a core Flight System (cFS) application that is a plug in to the Core Flight Executive (cFE) component of the cFS. The cFS is a platform and project independent reusable software framework and set of reusable applications developed by NASA Goddard Space Flight Center. -
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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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CODEIT-IDE
CODEIT is a simple IDE, You can handle Javascript, HTML, PHP , CSS, SQ
CODEIT is a simple IDE to develop HTML5 applications directly online in Your browser (best use with Google Chrome). Thanks to the Codemirror library developed by Marijn Haverbeke (codemirror.net) and the initial founder XO Systems, we have created/updated our online IDE with everything you need for the development. -
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Molecular Dreams
C++ High level framework thinked for javascript
Molecular-Dreams permits to develop applications of all kinds, using C++ and/or simply Javascript code; basically, Md makes a simple abstraction of varoius complex-works-flow around QObjects and associates. Md proposes a HighLevel RDBMS based on QtSQlite driver, adding something to it! It also will make an using-abstraction of various C libraries as RtAudio, Ogg, Vorbis, Speex, Flac and LibAv. Molecular-Dreams was developed on Linux, but it could be easily ported to other platforms, as MacOSX, Windows, Android and others. ... -
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trj_cavity finds protein cavities throughout Molecular Dynamics (MD) simulation trajectories. The program works with files in PDB format, but it also can read/generate GROMACS compatible formats such as XTC. The same project can be compiled as a GROMACS tool or as a standalone version. Installation instructions are provided in the INSTALL file of the project and in https://sourceforge.net/p/trjcavity/wiki/Home/#ffad If you need support using this tool (or report bugs), please post it in the discussion forum. ...
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GEDI (Groundtruthing Environment for Document Images) is a highly configurable document image annotation tool. Its basic structure involves two types of files, an Image file, and a corresponding .XML file in GEDI format. LAMP Univ of MD, College Park, MD
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LORE
Another RAID Driver for Linux
LORE (Layer Of Raid Engine) is a software RAID driver for Linux like MD. LORE delivers better performance than MD in various worklaods. -
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Chuyu
VC 140 LTL
...使用方式： 你现在工程下面建个 VC140LTL文件夹，然后将本工程所有文件丢到里面 项目属性，C/C++目录， 包含目录 中增加 $(WindowsSDK_IncludePath) $(SolutionDir)\VC140LTL 最后去掉 从父级或者默认设置中继承，点击确定 然后在你的stdafx.h中增加 #include <_msvcrt.h> 然后在你的stdafx.cpp中增加 #include <_msvcrt.cpp> 在吧工程设置为动态链接（MD），在重新编译，即可得到轻巧的exe -
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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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LSDMap
Locally-Scaled Diffusion Maps from molecular dynamics trajectories
...The eigenvectors of the diffusion matrix can be used to form a small set of reaction coordinates describing the behaviour of a high-dimensional data set such as an equilibrium MD trajectory. -
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MD PnP | OpenICE
Open Source Integrated Clinical Environment
As of 2015-06-23, this project may now be found at http://www.github.com/mdpnp/mdpnp. A prototype reference implementation of the standard for the Integrated Clinical Environment (ASTM F2761-2009) -
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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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grcarma
A Tk frontend to MD trajectories analysis program carma
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PyInteraph
analysis of interaction networks in structural ensembles of proteins
PyInteraph is a software research tool for the analysis of structural communication protein ensembles. It has been designed to analyze MD and structural ensembles with attention to binary interactions between residues, such as hydrogen bonds, salt bridges, and hydrophobic interactions. Once the interactions have been calculated, it is able to use different classes of intra- and intermolecular interactions, combined or alone, to calculate comprehensive interaction graphs. -
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This space is not maintained anymore. If you want to get the latest updates on fpocket refer to https://github.com/Discngine/fpocket. Fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level.
