[gmx-users] RE:Blowing up follow-up
lloyd.riggs at gmx.ch
Fri Jun 4 08:01:55 CEST 2010
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.
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