I want to visualize Hbonds between water molecules in the water using VMD. I use Hbonds in create representation but cannot see the bonds in the 3d view. Any idea? I play around with cut-off distance, angle but no success.
Hi Meisan! This page might be useful for you: https://www.ks.uiuc.edu/Training/Tutorials/science/10Ala-tutorial/tutorial-html/node5.html
Thanks Inna Ermilova . I have read this before, but it does not work for me. I however load a lammps trajectory file and not a .dcd or .psf file format. Also, I think using this method we only are able to define hbonds between non-hydrogen atoms, am I correct?
The other issue is that atoms in my trajectory file are identified with numbers rather a name, like O H etc. So, how does lammps know if I have hydrogen in my system?
Thank you!
You are welcome! Well, Meisam, your original question was about visualization with VMD... If I had a problem with one trajectory format I would convert it to another one (like pdb-format) and see what will happen. You might need to do analysis of hydrogen bonds as well using VMD.
- Badges
- Science topic