> On Wed, 2006-07-05 at 15:11 +1000, Mark Abraham wrote: >> > 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. > That is what I expect. However I find some atoms are far away from > others from step38885.pdb even though I have used all-bonds constraint. > Do you have any idea what's going on? Thank you for your help!
I don't have many further ideas. You have a bunch of atoms that appear to have moved around messily. If your visual check of the trajectory is valid then there shouldn't be anything wrong with your topology, but it might be worth checking. Maybe try re-running the calculation keeping lots of velocities and positions so you can do restarts close to the problem area and get more info... 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
