Hello everyone.
When visualizing MD simulation results in VMD, I'm getting artificial bonds between atoms when loading .xtc trajectories after the .gro file, like you can see in attached file. These unwanted connections appear in non-initial frames. How can I properly display periodic systems in VMD to remove these artifacts while keeping real bonds?
Best regards,
Nadezhda
Nadezhda Andreeva This is not a problem. You need to use the gmx tools to remove this view.
Thank Dr. Lourival Rodrigues de Sousa Neto for your recommendation. I don't quite understand, do I need to convert the file to another format using the gmx tools? Or how to use it?
Nadezhda Andreeva In general, I was used to using the entire gmx trjconv pbc whole. I don't remember very well. let me know if you get
- Badges
- Science topic
- Similar topics
- Linguistics
- Philology
- Classical Philology
- Manuscripts