Re: AMBER: Heat capacity, diffusivity way off in this simulation of SPC/E water?

From: Steven Winfield <>
Date: Tue, 09 Oct 2007 11:06:53 +0100

Hi David,

Try turning down / turning off your thermostat to get a better
diffusivity. I noticed the same thing once with TIP3P and this turned
out to be the problem.


David Cerutti wrote:
> I'm posting this to the reflector to see if anyone else might have ideas.
> What I've got is a simulation that seems to produce very wrong heat
> capacity and diffusivity for SPC/E water. I've attached the topology
> and initial coordinate files for your perusal. In my calculations, I
> was careful to let the system come together (it's kind-of gaseous to
> begin with) before I started computing the diffusivity and heat
> capacity. In my calculations, I DO get the correct density and also I
> believe Hvap. But, the heat capacity I compute by varying the
> temperature to get (dH/dT)p is about 30% too low, and the diffusivity is
> also about 30% too low. I have re-run the problem with my own MD code,
> and I get correct results for SPC/E using the same analysis methods I
> applied to the AMBER outputs, so it would seem there truly is something
> strange about the AMBER simulation results this time. (Doubly so because
> I think I've seen published data using AMBER that gets all the right
> answers.)
> It might be most helpful here if someone could ignore the input file I
> provide and just write their own as they would do it to get Cp and
> diffusivity, then run a brief (100ps should suffice) simulation with the
> coordinates and topology I provide. I don't understand where my results
> could have gone so wrong.
> Thanks!
> Dave
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Received on Wed Oct 10 2007 - 06:07:45 PDT
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