[gmx-users] Weird configuration when pulling rate is small

[Ming Tang]

Dear Erik,

Thanks for your advice. I think you are right. However, when using -pbc whole, every chain is intact but the three chains separate in some frames; when using -pbc nojump, the collagen molecule is not intact (there is a small part stay in the other box ) either. If I fix one end, and use -pbc whole, the problem is fixed.
Thanks and regards,
Ming