[gmx-developers] Question on reasons for temperature control

[hess at sbc.su.se]

Hi,

I agree completely with this change.

Berk

> I'm adding in the velocity verlet/NVT/NPT documentation, and
> I've got a philosophical question about this paragraph in the manual:
>
> "For several reasons (drift during equilibration, drift as a result of
> force truncation and integration errors, heating due to external or
> frictional forces), it is necessary to control the temperature of the
> system. {\gromacs} can use either
> the {\em weak coupling} scheme of Berendsen~\cite{Berendsen84} or
> the extended ensemble Nos{\'e}-Hoover scheme~\cite{Nose84,Hoover85}."
>
> I think this could be a bit misleading.  The main reason for using an NVT
> ensemble instead of an NVE ensemble is that one is interested in
> thermodynamic quantities.   It's not really to make up for the fact that
> there might be errors in the integration.   While such errors may be
> unavoidable, and a reasonable cost to pay to get significant speedup in
> the
> results, using a thermostat to cover is really more of a bandaid that may
> do
> more to fix the symptoms (increasing simulation temperature) than actually
> fix the problem (errors in the physical dynamics).  Siphoning off energy
> that is being generated by simulation errors gives rise to a steady state
> system that is not technically in equilibrium. In most cases of interest,
> statistical error is greater than any error induced by this, but it's
> always
> a second best option to running a more accurate integration.
>
> I'd propose a change to something like this:
>
> "While direct use of molecular dynamics gives rise to the NVE (constant
> number, constant volume, constant energy ensemble), most quantities that
> we
> wish to calculate are from a constant temperature (NVT) ensemble.
> {\gromacs}
> can use either the {\em weak coupling} scheme of
> Berendsen~\cite{Berendsen84}, the extended ensemble Nos{\'e}-Hoover
> scheme~\cite{Nose84,Hoover85}, or the velocity rescaling
> scheme~\cite{Bussi2007a}.
>
> There are several other several reasons why it might be necessary to
> control
> the temperature of the system (drift during equilibration, drift as a
> result
> of force truncation and integration errors, heating due to external or
> frictional forces), but this is not entirely correct to do from a
> thermodynamic standpoint, and caution must be taking in interpreting the
> results."
>
> ~~~~~~~~~~~~
> Michael Shirts
> Assistant Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434)-243-1821
>
> --
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.
>