Re: [AMBER] How the box info is used

From: Ilyas Yildirim <>
Date: Wed, 3 Nov 2010 23:48:21 -0500 (CDT)

Bill - I am running a simulation using anisotropic scaling after Tom's
suggestion. I changed the procedure a little bit; I do a very quick
temperature increase of the system in NVT (1000 steps), then turn into NPT
with a pressure coupling constant taup = 3.0 (before, it was 2.0). It has
been over 200 ps, and the system does not show any vacuum bubbles at all!
I never had such vacuum bubble problem before, and that might be due to
the systems being solvated with water in all directions. So, if the system
is membrane like, anisotropic scaling looks like to be a solution to get
rid of this problem.

I will continue this simulation and will apply this new scaling method to
another system. One thing that I have seen in the system is that there is
a layer of water molecules stuck on each surface, which might be perfectly
normal because of the high vdw energy well of the surface atoms.

Thanks for your and Tom's suggestions. Best regards,

   Ilyas Yildirim, Ph.D.
   = Department of Chemistry - 2145 Sheridan Road =
   = Northwestern University - Evanston, IL 60208 =
   = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
   = =

On Wed, 3 Nov 2010, Bill Ross wrote:

> Ilyas,
> I would definitely start with Tom's idea of trying anisotropic scaling.
> If all else fails I would definitely try equilibrating with plain NPT
> at lower temperatures to see if you can get the right density before
> going to NVT and 300K to see if other problems develop.
> Another thing that might be interesting to try might be using just one
> plane of solute.
> One thing I would try is watching the trajectory in VMD to see the
> bubbles develop, in case that gives any idea.
> In any case, it is a novel problem.
> Bill
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Received on Wed Nov 03 2010 - 22:00:03 PDT
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