Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: vmd
shmoe6/NAMD-Config-Generator
Config file generator for easier simulations with the Nanoscale Molecular Dynamics (NAMD) software.
Language: Python - Size: 1.85 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 0 - Forks: 0
simongravelle/gallery
Molecular art
Language: Jupyter Notebook - Size: 112 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 3 - Forks: 0
van-richard/PL888
command-line interface configuration files
Language: Jupyter Notebook - Size: 583 KB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 0 - Forks: 0
AiMiDi/C4D_MMD_Tool
A plugin for Cinema 4D written in C++ is used to import MikuMikuDance data into Cinema 4D.
Language: C++ - Size: 360 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 118 - Forks: 15
lammpstutorials/lammpstutorials-inputs
LAMMPS input from lammpstutorials.github.io
Language: Jupyter Notebook - Size: 150 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 12 - Forks: 1
FateMurphy/CEEMDAN_LSTM
CEEMDAN_LSTM is a Python project for decomposition-integration forecasting models based on EMD methods and LSTM.
Language: Jupyter Notebook - Size: 15.3 MB - Last synced: 19 days ago - Pushed: 3 months ago - Stars: 190 - Forks: 40
MVRonkin/dsatools
Digital signal analysis library for python. The library includes such methods of the signal analysis, signal processing and signal parameter estimation as ARMA-based techniques; subspace-based techniques; matrix-pencil-based methods; singular-spectrum analysis (SSA); dynamic-mode decomposition (DMD); empirical mode decomposition; variational mode decomposition (EMD); empirical wavelet transform (EWT); Hilbert vibration decomposition (HVD) and many others.
Language: Jupyter Notebook - Size: 8.42 MB - Last synced: 20 days ago - Pushed: about 1 year ago - Stars: 118 - Forks: 26
vrcarva/vmdpy
Variational mode decomposition (VMD) in Python
Language: Python - Size: 13.7 KB - Last synced: 25 days ago - Pushed: almost 4 years ago - Stars: 298 - Forks: 54
dadaoqiuzhi/RMD_Digging
RMD_digging is aimed to provide pre-processing and post-processing tools for the reactive molecular dynamics (ReaxFF) simulations based on MATLAB language, including formatting the reactive force field parameters, statistic anasysis of structures, trajectories and mechanisms and output of the visualization files.
Language: MATLAB - Size: 8.86 MB - Last synced: 29 days ago - Pushed: 29 days ago - Stars: 27 - Forks: 5
JasonWeinzierl/myoglobin
Term Paper for PHYS 4500 using NAMD and VMD to study the structure of myoglobin
Language: TeX - Size: 182 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
Warpv/allatom-polymere-system-in-VMD
create allatom polymere system from .xyz file in VMD
Size: 32.2 KB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
jarvist/3D-Rashba-Pockets
Rendering 3D-Rashba-Pockets with the help of Julia and VMD
Language: Tcl - Size: 233 KB - Last synced: about 1 month ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0
Colvars/colvars
Collective variables library for molecular simulation and analysis programs
Language: C++ - Size: 41.4 MB - Last synced: about 2 months ago - Pushed: 2 months ago - Stars: 172 - Forks: 51
tlemmin/peptideBuilder
VMD plug-in for building a peptide ab initio from backbone torsion angles or secondary structure
Language: Rich Text Format - Size: 34.2 KB - Last synced: 2 months ago - Pushed: almost 4 years ago - Stars: 1 - Forks: 0
cameronabrams/psfgen 📦
TcL/VMD/psfgen/bash scripts for generating MD systems for use with NAMD
Language: Tcl - Size: 10.2 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 9 - Forks: 4
soft-matter-theory-at-icmab-csic/chitin_builder
Chitin builder: A code to build chitin atomistic structures in Visual Molecular Dynamics (VMD)
Language: Rich Text Format - Size: 15 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 2
vishnu-prasad-kurupath/cncgen
Generate Carbon Nano-Cones using VMD
Language: Tcl - Size: 16.6 KB - Last synced: 3 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0
Sarah-Hesham-2022/BioPhysics-Molecular-Dynamics-Simulation
Using VMD and NAMD for molecular dynamics simulation of protein PDB files.
Language: Tcl - Size: 57.3 MB - Last synced: 4 months ago - Pushed: over 1 year ago - Stars: 3 - Forks: 2
pratiman-de/pdb-to-xyz
A script to convert multiple pdb files to a single xyz file using VMD
Language: Tcl - Size: 1.95 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0
hustcxl/SP_Lib
Signal processing method and algorithm library
Size: 127 KB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 156 - Forks: 54
jiafuei/vmdrs-py
Variational Mode Decomposition in Python using the Rust vmd-rs crate
Language: Rust - Size: 60.5 KB - Last synced: 12 days ago - Pushed: 3 months ago - Stars: 1 - Forks: 1
paralleltree/Scallion
.NET用MikuMikuDanceラッパーライブラリ
Language: C# - Size: 128 KB - Last synced: 28 days ago - Pushed: almost 2 years ago - Stars: 16 - Forks: 4
Hamid-Nasiri/VMD-MFRFNN
VMD-MFRFNN
Language: MATLAB - Size: 51.8 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 39 - Forks: 5
miu200521358/vmd_sizing
vmd(MMDモーションデータ)を、指定されたモデルに適用したサイズで再生成します。
Language: Python - Size: 6.22 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 61 - Forks: 14
AkiKurisu/UnityChanDance
Unity Chan Dance ! Unity MMD Player Project
Language: C# - Size: 261 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 3 - Forks: 0
anjibabuIITK/CLUSTER-ANALYSIS-USING-VMD-TCL
Kapakayala Anji Babu , IIT Kanpur, India.
Language: Tcl - Size: 416 KB - Last synced: 9 months ago - Pushed: almost 6 years ago - Stars: 6 - Forks: 4
smsaladi/vmd_viridis
Colorblind-friendly, perceptually uniform palettes for vmd
Language: Tcl - Size: 9.77 KB - Last synced: 9 months ago - Pushed: over 3 years ago - Stars: 2 - Forks: 0
joshua-mae/HoleHelper
VMD plugin with GUI and CLI utilizing HOLE2 without the MDAnalysis learning curve
Language: Tcl - Size: 67.7 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0
aslozada/tc
Display the VMD "dynamic" Field (beta, charge, occupancy, ...)
Language: Tcl - Size: 57.6 KB - Last synced: 6 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0
jiafuei/vmd-rs
Variational Mode Decomposition in Rust.
Language: Rust - Size: 28.3 KB - Last synced: 12 days ago - Pushed: 10 months ago - Stars: 0 - Forks: 0
superowner/MMD4MecanimLit
Convert vmd file to csv and used for Unity Mecanim,such as morph,motion
Size: 1.95 KB - Last synced: 20 days ago - Pushed: about 6 years ago - Stars: 4 - Forks: 1
mrat1618/oniom-vmd-visualisation
Visualise Gaussian ONIOM inputs in VMD
Language: Python - Size: 958 KB - Last synced: 10 months ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0
trishnasaha/3rd_PhD_Project_Virtual_Screening_Arginase_Inhibitor
Autodock-Vina, NAMD, VMD
Language: Perl - Size: 330 KB - Last synced: 4 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0
luisico/clustering
VMD plugin to calculate and visualize clusters of conformations for a trajectory
Language: Tcl - Size: 353 KB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 16 - Forks: 8
reyk/meta-data
meta-data datasource for OpenBSD vmd(8)
Language: C - Size: 26.4 KB - Last synced: 24 days ago - Pushed: over 5 years ago - Stars: 19 - Forks: 2
NNairIITK/TCL_VMD_SCRIPTS
A few useful vmd trajectory analysis scripts
Language: Tcl - Size: 1.52 MB - Last synced: 9 months ago - Pushed: almost 5 years ago - Stars: 5 - Forks: 1
drippypale/structural-bio-project
This project consists of multiple tcl modules, which perform a few tasks on a given protein pdb file (NMR structure)
Language: Jupyter Notebook - Size: 555 KB - Last synced: 12 months ago - Pushed: 12 months ago - Stars: 0 - Forks: 0
pcyra2/MD_workshop
Homepage for the 2023 AODI workshop
Language: TeX - Size: 165 MB - Last synced: 12 months ago - Pushed: 12 months ago - Stars: 0 - Forks: 0
YarkaS/Scientific-Visualization-of-COVID-19-and-Influenza
Research on similarities and differences between COVID-19 and Influenza type A using VMD.
Language: TeX - Size: 5.69 MB - Last synced: 26 days ago - Pushed: over 3 years ago - Stars: 1 - Forks: 1
HJprint/University_project_vmd_majorization
使用vmd算法对含有噪声的图像信号进行分解，去除掉噪声信号，将剩余信号合成，得到去噪声图像。分别使用alo、ao、ga、gwo、mpa、spo、woa算法对vmd算法中的参数进行优化，实现快速、准确的完成图像信号的分解。
Language: MATLAB - Size: 8.78 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 6 - Forks: 3
Sarah-Hesham-2022/TCL-TK-VMD-PDB
TCL-TK for VMD.
Language: Tcl - Size: 230 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 3 - Forks: 0
errno-mmd/VMD-Lifting Fork of DenisTome/Lifting-from-the-Deep-release
VMD-Lifting is a fork of 'Lifting from the Deep' that outputs estimated 3D pose data to a VMD file
Language: Python - Size: 1.01 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 37 - Forks: 6
JayLau123/Create-Lammps-input-files-with-packmol-and-VMD-
Simulation of water molecules with packmol, VMD, and Lammps.
Language: Jupyter Notebook - Size: 6.9 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
luisico/rmsdtt
VMD plugin for rmsd calculation and fitting of molecular structures
Language: Tcl - Size: 375 KB - Last synced: 7 months ago - Pushed: almost 10 years ago - Stars: 3 - Forks: 2
naotohori/vmd-scripts
VMD scripts
Language: Tcl - Size: 202 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 5 - Forks: 2
VirtualLiveLab/vmdtofbx
VMDのモーフデータをFBXに変換するためのプロジェクト
Language: C++ - Size: 79.1 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 5 - Forks: 0
seanlynch/godot_pmx_importer
Development on this project is happening on the V-Sekai fork at https://github.com/V-Sekai/godot-pmx .
Language: C++ - Size: 286 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 2 - Forks: 2
aaaastark/hybrid-model-with-cnn-lstm-python
Hybrid Model with CNN and LSTM for VMD dataset using Python
Size: 14.4 MB - Last synced: 11 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 1
genchik1/Phonon-spectrum-of-graphene-in-Lammps
:snowflake: Phonon spectrum of graphene and a new quasi-two-dimensional structure in LAMMPS
Size: 58.6 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0
azimatarannum/Octane_Water
Octane in a water box under CHARMM36 forcefield
Size: 16.8 MB - Last synced: 2 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0
Rohith-2/VMD-Embedding
Application of VMD in NLP via TF-IDF for better semantic relationships.
Language: Jupyter Notebook - Size: 28.1 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 1
emleddin/comp-chem-website
A Jekyll website for the research guides--UNIX, AMBER, Analysis, and R.
Language: CSS - Size: 30.8 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 4 - Forks: 0
luisico/itrajcomp
interactive Trajectory Comparison
Language: Tcl - Size: 395 KB - Last synced: 7 months ago - Pushed: almost 10 years ago - Stars: 1 - Forks: 0
luisico/swap
VMD plugin to swap coordinates between atoms in a molecule
Language: Tcl - Size: 129 KB - Last synced: about 1 year ago - Pushed: almost 10 years ago - Stars: 0 - Forks: 1
onlyuser/MMDLoader Fork of syoyo/MMDLoader
Simple MMD(PMD/VMD) loader in C++
Language: C++ - Size: 3.03 MB - Last synced: about 1 year ago - Pushed: over 7 years ago - Stars: 4 - Forks: 1
kenneym/vmd-cudagl
Dockerized VMD images, equipped with OpenGL rendering and CUDA Acceleration
Size: 65.7 MB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 2 - Forks: 0
krassowski/vmd-agr-parser
Simple script for plotting .agr (Grace) files created with VMD (Visual Molecular Dynamics). Allows export to csv/svg/png.
Language: Python - Size: 130 KB - Last synced: about 1 month ago - Pushed: about 4 years ago - Stars: 1 - Forks: 1
rajikaimal/sublime-vmd
:snowflake: Sublime Text 3 plugin for vmd
Language: Python - Size: 2.93 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 2 - Forks: 0
