Here are some notes on my preferences for rendering with VMD’s tachyon. For example, this comparison of some proteins was made with the Space Filling method below: Space Filling (good for proteins) Choose VDW Drawing Method with AOChalky as the material (Graphics->Representation…). Turn ofo axes (Display->Axes->off) Enable shadows and ambient occlusion (Display->Display Settings…) Make carbon gray (Graphics->Colors). Choose name “C” and change it to gray. (Optional) Change background to white (in colors, Display->Background) Render (File->Render…) and choose Tachyon as the rendering engine. See how to change image size (Optional) The default colors in VMD are over-saturated. You can open with...
Here are two example scripts for making movies in VMD. The first is shown below and the other controls the camera to follow an interesting part of the simulation. Rotate and Change Representation This script makes a movie of the molecule rotating and stops halfway to change the representation. Most of the script is set-up. The loop to make the movie starts on line 75. Expand Script Complex Camera Movement This script follows a list of key-points with the camera given by an external file (called hindices.txt). In the example, the camera is following the positive charge site of a...
This tutorial will show you how to reproduce the method in the recent White et al. water AIMD paper (White et al., 2017). The goal of the method is to minimally bias a water simulation to match a reference RDF. We will first convert a reference RDF into a set of reference scalar coordination number moments. Then, an NVT simulation is run to find a minimal bias which causes the coordination numbers to match their reference values. It won’t be covered here, but the bias can then be used to run NVE simulations or in conjunction with other free-energy methods....