The script below starts the VMD container and runs the xxx.vmd script from your workspace directory. Note you could also point the CLI command to launch VMD on a script located in your working directory instead.
The current working directory accessible within the container as "/workspace": docker run -ti -gpus all -rm -v $(pwd):/workspace nvcr.io/hpc/vmd:1.9.4a44 vmd To run the VMD container from the CLI, issue the following command, which runs VMD and makes You can run the VMD container interactively within the container.You can run VMD directly from the docker run command.There are two options to run the VMD container. Pascal(sm60), Volta(sm70), or Ampere (sm80) NVIDIA GPU(s).One of the following container runtimes.System requirementsīefore running the NGC RELION container please ensure your system meets the following requirements. See here for a document describing the steps to pull NGC containers. See here for a document describing prerequisites and setup steps for all HPC containers. VMD, tutorials, and documentation are available at While VMD 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 run on both workstations (or single cluster nodes) and in parallel on distributed memory clusters and supercomputers using MPI. In particular, VMD 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. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. VMD provides a wide variety of graphical representations for visualizing and coloring molecular structures: molecular surfaces, space-filling CPK spheres and cylinders, licorice bonds, backbone tubes, and ribbons, secondary structure cartoons, and others. VMD is designed for modeling, visualization, and analysis of biomolecular systems such as proteins, nucleic acids, lipid membranes, carbohydrate structures, etc.
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