[gmx-users] RE:Blowing up follow-up

[lloyd riggs]

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
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