Does the use of *addIons2* in place of *addIons *not solve the issue?
Hirdesh
On Fri, Jul 22, 2011 at 6:00 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Thu, Jul 21, 2011, Wei Chen wrote:
> >
> > After I solvated my protein, I used "addIons" to add ions to the
> > system to reach certain ion concentration. I found that some ions were
> > placed outside of the water box. Is this normal? When I used AMBER8
> > long time ago, this did not happen. I was wondering if this is
> > something with the new version of AmberTools.
>
> It's been seen before I think: http://archive.ambermd.org/201007/0205.html
>
> (Just use the search box on the Amber mailing list web page). But I don't
> know that it was ever resolved, so if Dan is willing to look at it, that is
> fine. Presumably, (a) most people never study the distribution of ions too
> closely, and/or (b) equilibration makes the simulation forget about the
> details of the intial condition anyway.
>
> ....dac
>
>
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Received on Fri Jul 22 2011 - 06:00:04 PDT
