From: Aron Broom (broomsday_at_gmail.com)
Date: Wed Oct 24 2012 - 17:04:54 CDT
I thought that TIP4P was parameterized as a rigid molecule? Anyway,
related to this topic, I see you have "langevinHydrogen off", which means
the thermostat doesn't apply itself to the hydrogens. In the case where
TIP4P is rigid, this would be ok, but now those hydrogens aren't rigid, so
maybe try "langevinHydrogen on" (comes with an ~5% performance penalty) or
Honestly I don't see how either of the above things I'm suggesting would
solve a problem of this magnitude, but I think they are important anyway.
So, how did you convert your TIP3P simulation to TIP4P? Did you take out
the peptide and re-solvate with TIP4P? Or did you just rename the waters
and toss in a forth point? If the latter is the case, then I can imagine
the coordinates for the 4 points of the water might be starting fairly
messed up, and you would want to energy minimize for AT LEAST 1 step per
water molecule. Maybe I'm crazy on that, but this really seems like it
might just be a poorly minimized system, no?
On Wed, Oct 24, 2012 at 4:00 PM, Jesper Sørensen <jesorensen_at_ucsd.edu>wrote:
> Hi Aron,
> You probably did this but just in case:
> When you generated your prmtop did you set "set default FlexibleWater on"
> in LEaP?
> http://ambermd.org/namd/namd_amber.html, section 5
> On Oct 24, 2012, at 8:26 AM, Aron Broom <broomsday_at_gmail.com> wrote:
> Did you tell NAMD you are using TIP4P? you have to put "waterModel tip4"
> in your config file, the default is tip3.
> 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
>> 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,
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> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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