VMD

VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. 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 remote computer. ( taken from VMD's web site )

 

Setup

VMD is currently available with reduced functionality, while we are preparing the EGL (GPU-accelerated) support. VMD can run in batch mode, with the Tachyon renderer. Simply load the corresponding module.


		
			

module load VMD

While the deployment of OpenGL-assisted rendering is still in progress on the new daint, users can already take advantage of another NVIDIA library for ray-traced image production.

VMD includes a built-in GPU-accelerated version of the Tachyon ray tracing engine, using NVIDIA CUDA and OptiX to achieve performance levels up to six times faster than the previous CPU versions of Tachyon. The new renderer is labelled "TachyonL-OptiX" in the VMD renderer window, and it supports the vast majority of Tachyon rendering features, with emphasis on ambient occlusion lighting, shadows, depth-of-field, high quality transparent surface rendering, and parallel rendering.

Details are found on the VMD web site, here:

The new syntax in your Tcl script would be:


		
			

render TachyonLOptiXInternal my_image.ppm