Mark, I have written a new force field for my polymer. I have used this force field for polymer in water. It worked fine. When I tried to put polymer with nanotube in water, then I had this strange problem (My force field worked fine for nanotube alone). Anyway I will try to rerun it.
Thank you for your help! Dongsheng On Wed, 2006-07-05 at 16:04 +1000, Mark Abraham wrote: > > 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 _______________________________________________ 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
