>An output coordinate file is always produced unless mdrun completely fails and >seg faults. That doesn't mean the coordinates are sane. It's meant to help you >diagnose in cases like this where you have an absurd force on some atom.
>What is atom 2832? What's around it? Is there anything obviously clashing with >it? Also check the topology for errors. >-Justin The atom is the iron that I introduced. It is bound to an oxygen which is itself bound to the carbon of a ring. It is found on the spot where the ligand, not introduced in the simulation yet, is binding to the protein. There are a few carbons and nitrogens but nothing in close proximity or clashing with it. The topology seems ok to me. This is the link to the file, the iron shows a charge of +3, could this be the cause of such a great force? https://drive.google.com/file/d/0Bxa-J2wEpEeqTC1UX2tNOG1LVms/edit?usp=sharing Thank you again, Nicholas -- 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.
