Hi, I have a capped amino acid in box of water and ion(but the system is not charged) and named it initial.gro, i can see some unreal bonds when i open it with VMD(H atom has 2 bonds!). And when i open it with gaussview C and H atom where nonbobded and were single atoms around remained bonded structure.( maybe aminoacid in initial.gro file didn't get well optimized or anything... )
But when i run nvt, the amino acid structure get real structure and everything is ok. I remember Justin said that MD and GROMACS can't make or break bond. So What happend to my system? Best regards -- 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.