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

From: David A Case <>
Date: Thu, 26 Nov 2015 11:26:11 -0700

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 SHAKE.
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

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?


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Received on Thu Nov 26 2015 - 10:30:02 PST
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