From: Aron Broom (broomsday_at_gmail.com)
Date: Wed Mar 27 2013 - 12:20:30 CDT
Also, are you using a GPU?
And, are you intending to set the cutoff to something approximately
infinite (9999 or somesuch)? Keep in mind that with implicit solvent you
no longer have the ability to use PME, so if any nonbonded interactions get
cutoff, it could be problematic, though it might not matter that much
depending on what you are doing.
On Wed, Mar 27, 2013 at 12:31 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Wed, Mar 27, 2013 at 5:27 PM, Fugui <theoreticalchem_at_163.com> wrote:
> > Dear NAMD users:
> > I will do an implicit solvent MD using NAMD, can anyone tell me the
> speed of
> > the implicit solvent MD compared to explicit solvent MD. I have a
> protein of
> > 300 amino acids.
> it will be faster.
> > BW
> > Fugui
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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