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!
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...
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
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!
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
Help, please...
https://www.researchgate.net/post/Problemas_con_solvatacion_automatica_en_VMD
- Badges
- Science topic