How to trace a single molecule and a defined radius around it throughout a trajectory in VMD?
I have a GROMACS trajectory of a system with various components and I want to follow a particular molecule (from which I have various in the topology) and the what other molecules appear in a defined radius around it throughout this trajectory. Specifically, I want to follow this single residue through time and the molecules that appear close to it in order to see how it enters micelles and orientates in those.
With the selection tool in visual molecular dynamics (VMD) I'm able to easily select a single residue, but not able to only see that residue and define a radius around it during the whole trajectory.
If you want only to visualize it. You can choose an atom in your molecule of interest (for example a central atom). In VMD:
graphical representation --> create representation (fo example index 1, your desired atom) --> drawing method VDW , material transparent, sphere scale (your desired radius). And run the movie, good luck!
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