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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Received on Tue Feb 21 2012 - 07:30:01 PST
