Gmx traj looks weird

User discussions
1

GROMACS version:2021
GROMACS modification: No
Here post your question

I am visualising my traj in vmd, after cat and centering,it looks like this

20241030_123609
20241030_1236091848×4000 1.22 MB

I have no idea why visualisation looks off. The gro files are fine.

Screenshot_20241030_124213_ChatGPT
Screenshot_20241030_124213_ChatGPT1080×493 129 KB

2

It doesn’t look like the most common visualization problems. However, to help you further it would be good to get either:

  • The command lines you used to convert the trajectory and especially how you opened the files (and which files you used as input) in VMD.

or

  • A link to download your files, if they are small enough to be downloaded easily.
3

Hi thank you. I figured out the error was due to a corrupt topology file through which xtc was loaded in vmd.