If you plan on using PME, that means you are representing the solvent
explicitly. However, you are never actually adding explicit solvent to
your system.
Your setBox command will simply draw a box around your molecule making sure
that the center of every atom is inside -- probably not what you want. If
you plan on solvating your hexane in water (or any other solvent, for that
matter), look at the command solvateBox or solvateOct.
You can't run PME with most codes on a single molecule of hexane.
HTH,
Jason
On Sat, Feb 2, 2013 at 2:36 PM, Jonathan Saboury <jsabou1.gmail.com> wrote:
> Hello AMBER users,
>
> I am having problems setting up a period box around my compound of
> interest. I am using the command "setBox HEX centers" (where HEX =
> hexane.mol2) but the box is way too small (less than the size of a hydrogen
> atom).
>
> My problem and my pathway to it is greatly detailed in "
> https://simtk.org/forums/viewtopic.php?f=161&t=3901&start=10#p8809".
>
> Thanks!
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Feb 02 2013 - 13:00:02 PST
