Re: [AMBER] heat capacity

From: David A Case <>
Date: Sat, 21 Mar 2015 09:17:25 -0400

On Fri, Mar 20, 2015, Ahmet yıldırım wrote:

> I am trying to calculate the heat capacity at constant volume of 1000 water
> molecules (tip3p). Firstly I did 10 ns NPT simulation, with
> Parinello-Rahman Barostat. And then I performed 100 ps NVT simulation, with
> saving time 5 fs. But the pressure of system fluctuates about 100 bar at
> NVT simulation. That means the system hasn't reached equilibrium. And the
> heat capacity results are not in good agreement with experiment.
> -The pressure fluctuations of 100 bar are normal for a normal MD
> simulation, right? But it isn't normal for NVT simulation?

High pressure fluctuations are normal for all MD simulations.

In NVT simulations, Amber by default does not compute or print pressures, so
I'm guessing most people on the list don't know exactly what on should
suspect. We do this routinely for crystal simulations, and fluctuations of
several hundred atm and average values between -100 and +100 are generally

> -Which the barostat and thermostat do you suggest for NPT simulation? And
> why?

For Amber, I'd recommend the Langevin thermostat and the Monte Carlo barostat.
They should both give good estimates of the canoncial ensemble. See the
following paper for information about how to test the results of *your*

%A M.R. Shirts
%T Simple Quantitative Tests to Validate Sampling from Thermodynamic Ensembles
%J J. Chem. Theory Comput.
%V 9
%P 909-926
%D 2012

Note that 1000 molecules is at the lower edge of size that won't have
artefacts. We generally use boxed with about 4000 water molecules.

> can you please suggest me some good
> "Thermodynamic/Statistical Physics" and "Statistical Physics of Proteins"
> books explaining the heat capacity, entropy, partition function and free
> energy topics. It will be good if they include both theory and the story of
> theory (equation). Especially the story is very important :)

See the books by Tuckerman or by Frankel & Schmid. Both of lots of technical
details about subjects like this. But nothing beats personal experience.
There are tons of papers about the equilibrium properties of TIP3P water; make
sure that you can reproduce literature results.


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Received on Sat Mar 21 2015 - 06:30:03 PDT
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