From: Aron Broom (broomsday_at_gmail.com)
Date: Wed Oct 24 2012 - 10:26:43 CDT
Did you tell NAMD you are using TIP4P? you have to put "waterModel tip4" in
your config file, the default is tip3.
~Aron
On Wed, Oct 24, 2012 at 10:55 AM, Martin, Erik W <Erik.Martin_at_stjude.org>wrote:
>
> I'm hoping someone on this list will have some insight on this problem
> I've been having. I'm running a simulation of an 82aa peptide in a
> truncated octahedron water box for a total of ~100k atoms. I'm also using
> an AMBER ff. I have been running this simulation for ~25ns using tip3
> water with no problems at all. However, I wanted to run this with tip4
> water as well and am seemingly incapable of getting it to equilibrate
> properly.
>
> On the first structure, I was able to equilibrate it by constraining
> peptide coordinates and allowing the water – with rigid bonds – to
> equilibrate in the cell. When I rebuilt the system with tip4 water I did
> absolutely nothing different. It runs fine with rigid bonds on and the
> peptide constrained, but when I try to allow it to run I get the dreaded
> "atoms moving too fast" error at about step 120-200. It is different atoms
> every time, and what seems to be happening is that the temperature and
> pressure both ramp up to enormous values. (for the record, I'm using
> Langevin dynamics to control temp and pressure)
>
> Does anyone have a clue what could be causing this condition?
>
> Thanks a lot,
> Erik
>
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-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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