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

From: David Cerutti <>
Date: Mon, 8 Oct 2007 22:25:43 -0700 (PDT)

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.



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Received on Wed Oct 10 2007 - 06:07:40 PDT
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