Yes, it's true, the test is fairly simple, I was just hoping to avoid the
work. I'm posting this reply such anyone searching the archive can confirm
that it is possible to fake vacuum simulation using igb and extdiel=1.0 in
the amber11 pmemd.cuda code.
So the result is that you can indeed fake the igb=6 when using pmemd.cuda
by using something like igb=1, extdiel=1.0.
I tested three conditions on the CPU using sander:
1) igb=1
2) igb=1, extdiel=1.0 (the fake case)
3) igb=6
After 10 ps, the coordinates for igb=6 and the fake case are identical
across ~8000 atoms, 100% identical. for the normal igb=1 control, the
coordinates are dramatically different. All runs had the ig variable set
to the same value.
So that confirms that using a GB model with both the external and internal
dielectric set as 1.0 essentially fakes being in a vacuum. The speed on
the GPU is fairly decent also.
~Aron
On Thu, Feb 23, 2012 at 2:09 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Tue, Feb 21, 2012, Aron Broom wrote:
>
> > 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?
>
> Isn't it pretty easy to just try it and see what you get? You have the
> CPU result for vacuum, so you can test both accuracy and timings with what
> you propose.
>
> ...dac
>
>
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>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Sat Feb 25 2012 - 22:00:02 PST
