VMD-L Mailing List

From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Wed Nov 24 2021 - 14:20:11 CST

Hello All
Just curious if anyone has coded up a plugin to read gromacs connectivity information from either top or tpr files?
Using the gro file as the source of truth creates bonds according to the bond table in VMD which may work most of the time. However, there are cases for instances where a gromacs simulation explodes and the resulting debug pdb step files that are written can appear pretty strange in vmd and complicate forensics.

Reading through the list i found a number of entries with gromacs mentioned, although none contained a conversation about gromacs reading topology files.

If I missed something please let me know by replying with the RTM and a possible page link.

thank you
happy thanksgiving
brian