> Mark, > > Thank you for your reply. When I checked step38885.pdb, I found a > polymer chain in my system fall apart (bond broken). If I visualize the > trajectory. it is fine till step38000 (last frame in my trr file).
OK... bonds don't just "break" in MD simulations. Bonded potentials don't allow for it, and often bond-length constraint algorithms are being used anyway. If you're not using such algorithms, it might be helpful to look at the time evolution of the bond length of the bond that breaks. I have heard of weird cases where some resonance got established in the system eventually leading to some catastrophic failure (think Tacoma Narrows Suspension Bridge!) - if so then the time evolution should show such behaviour. I can't explain the KE doubling though... Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
