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VMD is a molecular visualization program designed for the modeling, visualization, and analysis of biomolecular systems such as proteins, nucleic acids, lipid membranes, and carbohydrate structures. It provides a wide variety of graphical representations for visualizing and coloring molecular structures: molecular surfaces, space-filling Corey-Pauling-Koltun (CPK) spheres and cylinders, licorice bonds, backbone tubes and ribbons, secondary structure cartoons, and others.
VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, it can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a local or remote computer.
While the program is typically used interactively in a desktop graphical environment, it can also be used to perform non-interactive (batch-mode) analytical calculations and visualization tasks on workstations (or single-cluster nodes) and in parallel on distributed memory clusters and supercomputers using messaging passing interface (MPI). Visit the VMD website for more information.
Installation
You have the option to download and install VMD on bare-metal or pull and run the VMD container from NVIDIA GPU Cloud.
Installing applications in a high performance computing (HPC) environment can be challenging. Containers let you run the application without installing it on the system, making it easy to deploy the most recent version of the application while optimizing performance. Furthermore, running a VMD container is very straightforward and can be set up in minutes.
Running Jobs
Once you pull the container from NGC, there are two options to run it.
- Run VMD directly from the nvidia-docker run command.
- Run the VMD container interactively within the container.
1. Running VMD from the Command Line
To run the VMD container from the command-line interface (CLI), issue the following command, which runs VMD and makes the current working directory accessible within the container as "/workspace":
nvidia-docker run -it --rm -v $(pwd):/workspace nvcr.io/hpc/vmd:cuda9-ubuntu1604-egl-1.9.4a17 /opt/vmd/bin/vmd -dispdev openglpbuffer
Note that you could also point the CLI command to launch VMD on a script located in your working directory instead. The script below starts the VMD container and runs the xxx.vmd script from your workspace directory:
nvidia-docker run -it --rm -v $(pwd):/workspace nvcr.io/hpc/vmd:cuda9-ubuntu1604-egl-1.9.4a17 /opt/vmd/bin/vmd -dispdev openglpbuffer -e /workspace/xxx.vmd
2. Running VMD Interactively
In this example, we’ll run VMD interactively and reproduce an H1N1 test scene included within the container. Running interactively is useful when using VMD for visualization and analysis tasks that may involve external scripting of VMD runs, significant file management within complex directory hierarchies, or running multiple VMD instances within the same container and operating system (OS) image.
To run the VMD container interactively, issue the following command, which starts the container and also mounts your current directory to /workspace so it’s available inside the container. (See the -v options on the command below to set the mapping of your local data directory to the one inside container.)
nvidia-docker run -it --rm -v $(pwd):/workspace nvcr.io/hpc/vmd:cuda9-ubuntu1604-egl-1.9.4a17 /bin/bash
After the container starts, you’ll be in the /directory and can then change to /opt/vmd/h1n1testscene to re-render the H1N1 test scene, and VMD can be launched. Run the H1N1 test scene included inside the container. The H1N1 test scene demonstrates the "QuickSurf" NVIDIA® CUDA®-accelerated molecular surface calculation, user-defined labels and graphical geometry, and Epison Generation Language (EGL)-based off-screen OpenGL rendering:
cd /opt/vmd/h1n1testscene
/opt/vmd/bin/vmd -dispdev openglpbuffer -e h1n1-egloptix-test.vmd
After the H1N1 scene has been loaded and rendered, VMD will write out the image to a file named "vmdscene-egl.tga." That can then be copied to /workspace so that you can copy the resulting image to storage external to the container for viewing.
Test Setup
The container contains scripts to run and test VMD. Run the HIV-1 capsid test scene included inside the container. This test scene demonstrates the "QuickSurf" CUDA-accelerated molecular surface calculation, EGL-based off-screen OpenGL rendering, and OptiX GPU-accelerated high-fidelity ray tracing:
cd /opt/vmd/hivtestscene
/opt/vmd/bin/vmd -dispdev openglpbuffer -e hiv-simple-egloptix-test.vmd
Recommended System Configurations
The VMD container is optimized and tested for reliability to run on NVIDIA® Pascal™- and NVIDIA Volta-powered systems with CUDA® 9 or newer. VMD and all the HPC application containers available on NVIDIA GPU Cloud can run on the following systems:
- Workstation: Powered by NVIDIA Titan V and x86 CPU
- NVIDIA® DGX™ Systems
- HPC cluster with Pascal/Volta GPUs, CUDA 9, x86 CPU
- Cloud (AWS, Google Cloud Platform and more)