[gmx-developers] Which integrator/coupling for accurate fluctuations?

[Teemu Murtola]

Hi,

On Wed, Jan 27, 2010 at 20:47, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Initial tries with Leap Frog/Nose Hoover/Parrinello Rahman give us
> fluctuations that are quite a bit too large (using GAFF):
> methanol: cp_exp=81, cp_gaff=141
> ethanol:cp_exp=122, cp_gaff=211
>
> This is from equilibrated boxes with 512 molecules. Any hints, suggestions?

I could also comment on this, because I worked on similar problems a
few months back.

Notice how the values you give are very close to 3*R*natoms+R, which
is the Cp you would expect for a completely classical system without
any constraints (so I'm assuming you are not using bond constraints,
and that you haven't applied any quantum corrections). So although
some algorithmic improvements can improve things a bit, it's probably
the physics of your model that is the reason for the larger heat
capacities. In reality, bond vibrations (and most of angle vibrations
as well) have too high frequencies to be excited in room temperature,
and even for dihedral rotations QM effects give a significant
contribution to the heat capacity.

In my experience, the QM effects could easily make up the difference
you have between the experimental and the simulated values, but
calculating more than a simple estimate for them is probably not easy.
On the other hand, if you are not interested in the effects of
intramolecular degrees of freedom on the heat capacity, you could
calculate the fluctuations of just the intermolecular enthalpy, and
then add the heat capacity of a gaseous substance to get the
intramolecular contribution.

- Teemu