Question
Asked 1st Mar, 2019

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.
Thanks for the help!

Most recent answer

All Answers (5)

2nd Mar, 2019
Ramin Ekhteiari Salmas
King's College London
protein within 6 of residue 2
It shows the the protein atoms (can be changed to any other selections) within 6 A of the residue 2. just an example...
3rd Mar, 2019
Tasneem Kausar
Aligarh Muslim University
If you want to check throughout trajectory, you need to write a script so that the x molecules around y residue of interest can be written throughout trajectory. This link can be helpful. https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/23723.html
3rd Mar, 2019
L. América Chi
Instituto Politécnico Nacional
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!
14th Mar, 2019
Henrique Bastos
Deakin University
Thanks for the help! In my case I wanted to follow a single molecule entering a micelle, so the final command was:
(all exwithin "distance" of residue "number") and name "X"
-exwithin to maintain different colors for the actual molecule
-residue number to select an atom of the molecule I wanted to follow
-X to ensure that of the selection "all", only the micelle molecules were detected

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