Hi Axel,
Thanks for your reply.
I am using extended CHARMM forcefield (with additional topology and parameters for Hydroxyproline) to model collagen molecule. What checks do I need to make to see improper initial coordinates if it is due to that?
Have you looked at (visualized) your DATA file yet?
If it helps, I attached a short README file how to do this using VMD &
topotools. (I've been spamming this a lot lately. Steps 3 and 4
discusses how to check the boundary conditions.)
Cheers
Andrew
README_visualize.txt (2.85 KB)