Respected sir/ma’am,
I am using coarse-grained model on lipid bilayer in gromacs. I have the .gro files when I am trying to visualize it in vmd, the bonds between the beads are not showing. So, please if anyone can suggest me how to visualize the bonds between two beads or what dependency should I have to upload with .gro that will be helpfull.
Thanking You
Sankar Maity
Dear @sankar
VMD in general doesn’t know what bonds are or where they are supposed to be (for example, this information is not reported in the .gro file), but it guesses them depending on the distance between the atoms.
In coarse grained systems the beads are far and VMD doesn’t read them as part of the same molecule, so you will see only beads with no structure. There are scripts to fix this which are made available by the martini people, like here for example.
Respect sir/ma’am,
Thank you, for providing this link (Visualizing Martini (using VMD) – Martini Force Field Initiative) to me. I followed the process mentioned there, and it successfully resolved the issue I was experiencing.