Dear Gromacs Users, I did NPT simulations with a system containing 15000 atoms of polymers.
Initially, conf.gro was visualized in VMD and showed all connections are OK. However, the confout.gro (final output configuration) seems to look bad. Some of bonds are disconnected at the outer surface which I guess the boundary of simulation box. I think that this is due to the periodic boundary conditions. The question is, If I use the correct topology files, does the confout.gro file can be used for the further simulation no matter how the visualization look like? Thank you. Best regards, Changwoon Jang, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
