Dear All, I had posted a couple days ago reguarding my system blowing up, after energy minimizing the structure, adding waters, then adding ions. I had repeated this from scratch several times as per the instructions, and played with everything possible in the .mdp files.
I noticed in visual inspection when I add ions, they are taken not at random, but are placed randomly. I end up with a 10-15 Angstrom hole with nothing in it. I woundered how to get around this, as when I try to do a 100-200 step minimization of the system with ions and waters, or a really short run of any kind, the system blows up due to excessive forces on the solution. My only thoughts were to do it manually, but this is a bit of effort, and I do not think this would be appropriate if I have 10 similar systems and have to do this for each one? Any suggestions? I can also find the origional errors and post if necissary. Cheers, Stephan Watkins -- Sicherer, schneller und einfacher. Die aktuellen Internet-Browser - jetzt kostenlos herunterladen! http://portal.gmx.net/de/go/chbrowser -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
