VIAMD

Visual Interactive Analysis of Molecular Dynamics

VIAMD is an interactive analysis tool for molecular dynamics (MD) written in C/C++. VIAMD is developed in collaboration with the Department for Media and Information Technology (LIU, Norrköping) and the PDC Center for High Performance Computing (KTH, Stockholm). It exposes a rudementary script language that is used to declare operations which are performed over the frames of the trajectory. The results can then be viewed in the different windows exposed in the application.

Status

Running VIAMD

Windows

For windows, we recommend to use the latest binary available on the .

Ubuntu and MacOs

For Linux and MacOs, we recommend you to build VIAMD on your machine following the procedure below. MacOs is not actively tested.

Building

Step 1: Clone the repository:

(Make sure the fetch the submodules as well)

git clone --recurse-submodules https://github.com/scanberg/viamd.git

(Step 1.5: Install dependencies of external libs:glfw & nativefiledialog) (Only for linux users)

For Ubuntu or kbuntu:

libx11-dev
libxrandr-dev
libxinerama-dev
libxcursor-dev
libgtk-3-dev (recommended for ubuntu, use Zenity for kubuntu)
pkgconf
libhdf5-serial-dev (handling of hdf5 file for VeloxChem)

For CentOS:

mesa*
libXrandr*
libXext*
libX11*
libXi*
libstdc++-static
hdf5-devel (handling of hdf5 file for VeloxChem)

Example for Ubuntu: sudo apt-get install libx11-dev libxrandr-dev libxinerama-dev libxcursor-dev libgtk-3-dev pkgconf libhdf5-serial-dev

Example for CentOS: sudo yum libXrandr* libXext* libX11* libXi* mesa* libstdc++-static hdf5-devel

Step 2: Configure using CMAKE

https://cmake.org/ (Example using terminal and default build configuration for system)

cd viamd
mkdir build
cd build
cmake ..

Step 3: Build!

cmake --build .

Step 4: Run

cd bin
./viamd

Updating VIAMD

git pull --recurse-submodules

Repeat step 3 to compile!

Binaries for windows

https://github.com/scanberg/viamd/releases/

Documentation

Documentation about VIAMD is available on the github wiki. The two first chapters relate to the visual and analysis features respectively, where we highlight the interactive part of software. The third chapter focus on the VIAMD language used for scripting and the fourth chapter propose a serie of tutorial (under construction).

A series of videos is available on youtube.

Update

If you want to stay informed about the latest update of VIAMD, please register your email address to the form.

Citations:

General Framework:
- R Skånberg, I Hotz, A Ynnerman, M Linares, VIAMD: a Software for Visual Interactive Analysis of Molecular Dynamics, J. Chem. Inf. Model. 2023, 63, 23, 7382–7391 https://doi.org/10.1021/acs.jcim.3c01033
- R Skånberg, C König, P Norman, M Linares, D Jönsson, I Hotz, A Ynnerman, VIA-MD: Visual Interactive Analysis of Molecular Dynamics, 2018, Eurographics Proceedings, p. 19–27
Specific tool:
- Selection tool: Robin Skånberg, Mathieu Linares, Martin Falk, Ingrid Hotz, Anders Ynnerman, MolFind-Integrated Multi-Selection Schemes for Complex Molecular Structures, 2019, The Eurographics Association, p. 17-21
- Shape Space and Spatial Distribution Function: Robin Skånberg, Martin Falk, Mathieu Linares, Anders Ynnerman, Ingrid Hotz, Tracking Internal Frames of Reference for Consistent Molecular Distribution Functions, 2021, IEEE Transactions on Visualization and Computer Graphics, 28 (9), 3126-3137