Organometallic bonds not showing

GROMACS version: 2020.4
GROMACS modification: No

Hello all,

I’ve ran a quick simulation of an organosilver complex in water. The silver containing bonds do appear to be present as the relevant atoms maintain the correct distance/angles but a variety of different GUI’s do not show these bonds, just the atoms effectively floating. I’m assuming this is fine as it’s just the GUIs not “drawing” the bonds that are present, but I was curious if there’s a way to prove the bonds do exist? I’d imagine the gmx distance module could show that the bonds maintain the correct distance etc.

Thank you in advance
sam

The bonds defined in the topology are definitive. Visualization programs simply guess based on pre-programmed chemical knowledge, and Ag bonds are likely not something built in to most programs.

There are several utilities that can compute relevant distances, but yes, gmx distance is one.