Re: [AMBER] Equilibrium temperature is higher than the target temperature in Langevin dynamics

From: jinfeng liu <>
Date: Fri, 27 Nov 2015 14:16:33 +0800

Thanks for your very helpful advices. But I still have a little confusion.
I run a mechanical embedding QM/MM-like simulation, for QM waters, these is
not any constraint, and the intra- and interactions between QM waters are
described by QM; for MM waters, it is TIP3P water model without shake. And
I am more concerned about the properties of water in QM zone. Do you think
there is a serious problem here with TIP3P water model but without shake ?
I have a radius=20A water box, in which the QM zone is about radius=8A.

2015-11-27 2:26 GMT+08:00 David A Case <>:

> On Thu, Nov 26, 2015, jinfeng liu wrote:
> > Thanks for your reply. But sometimes I found that the liquid water
> dynamics
> > simulation without SHAKE would give more reasonable result, so I would
> > prefer to use SHAKE.
> As Dan said, you should not simulate a rigid water model without using
> If you need a model with better dynamics properties, consider alternatives
> like SPC/Eb or TIP4PEW. If you run TIP3P long enough without SHAKE, you
> will surely hit some crashes. Plus, important things like the density
> will be
> wrong.
> That said, even without SHAKE the average temperature should be OK. When
> you
> report the "equilibrium temperature", are you reporting the average T? Over
> how long a simulation? How big is your water box?
> ...thx..dac
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Received on Thu Nov 26 2015 - 22:30:03 PST
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