From: Axel Kohlmeyer (
Date: Thu May 23 2013 - 08:37:09 CDT

On Thu, May 23, 2013 at 2:40 PM, Michele Formica
<> wrote:
> Hello there everybody,
> I need to solvate my NP in a box of water. I created the *.psf and *.pdb
> file for the NP and the water box and followed the procedure here:
> but there's still water in the gold core of my NP.
> Two questions:
> What should I write where it says: [a b c alpha beta gamma} ?

that is only part of the command and the entire command line should
work "as is". why do you think it doesn't?

> What should I write where it says: set sel [atomselect $combined "not
> (same fragment as (exwithin $mindist of solute))"] ?

same thing as above. this line needs no change. why do you think so?

the example assumes that you know VMD scripting. if you don't i
strongly recommend you read the corresponding sections of the VMD
User's Guide and spend some time with the available VMD and Tcl


> Thanks, regards

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.