From: Andrews, Casey (
Date: Tue Nov 26 2013 - 17:53:02 CST


Currently we are trying to make visual images of a large system that contains a few millions of atoms. We would like to represent the molecules in each image as VDW. However, this takes a very long time to complete and seems to be only using one CPU core out of a possible 12. Additionally, the VDW representation does not seem to be taking advantage of the GPU we have installed (Nvidia Telsa 20C), but we know the GPU works because the Quicksurf representation uses it. We were curious if there was a way in which creating the VDW representation for millions of atoms could be made faster or if there was a faster alternative to VDW that would have the same visualization effect. We have tried to switch the render mode to GLSL but there wasn’t a huge speed increase in the VDW rendering process.

An additional question that we have is about the speed of the Tachyon rendering process on our large system. It appears that the scene parsing phase of the rendering process is only using one thread and it takes a very long time for each image. However once the scene parsing phase is completed, then the process is parallelized and happens quite quickly. Again we were wondering if there was a way in which the earlier stage of the process could be sped up?

For the rendering of these large systems, we have tried both VMD 1.9.1 and VMD 1.9.2. The OS we are using is Ubuntu version 13.10. Our Nvidia driver for the GPU is version 319.60 and our CUDA complier is release 5.0. Any help or guidance concerning the above issues would be greatly appreciated.

Thank you very much for your work on an amazing program,

Casey Andrews