Ahhh, yes that is clever. Thanks for the suggestion.
On Tue, Feb 21, 2012 at 10:17 AM, Giovanni Pavan <giovanni.pavan.supsi.ch>wrote:
> Hi,
> that's just probably a naive trick...
> but...what about putting an external ion maintained strongly restrained
> during the MD and at a distance > than the cutoff carrying a total charge
> opposite to that you need to place on the solute?
> It should work also with pmemd.cuda (with setbox for periodic boundary
> conditions) and would be faster than using a "fake" implicit solvent.
> Hope it works.
> Bye
> giovanni
>
> Dr. Giovanni M. Pavan
>
> SUPSI - Laboratory of Applied Mathematics and Physics (LaMFI)
> Centro Galleria 2, Manno 6928, Switzerland.
> e-mail: giovanni.pavan.supsi.ch
> web: http://www.dti.supsi.ch/~pavan/
> skype: giovanni_pavan
> phone: +41 58 666 65 60
>
> -----Messaggio originale-----
> Da: Aron Broom [mailto:broomsday.gmail.com]
> Inviato: marted́, 21. febbraio 2012 15:56
> A: AMBER Mailing List
> Oggetto: [AMBER] Faking Vacuum Simulations with a GPU
>
> I'm running a simulation on a system in a vacuum that sadly needs to have a
> net charge. This means the normal PMEMD isn't possible. There is a
> modification of the GB implicit solvent model, igb=6 that is said to do
> exactly this, but unfortunately it isn't currently implemented on the GPU.
> I'm wondering if anyone has thoughts on how bad it would be to simply do
> normal GB (igb=1 or 5 for instance), but set the external dielectric to
> 1.0?
>
> ~Aron
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
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--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Tue Feb 21 2012 - 08:00:02 PST
