[gmx-developers] Fluctuation properties

[Michael Shirts]

Hi, David-

> we are trying to get accurate fluctuation properties out of mdrun. For
> this purpose I have built in a calculation of the enthalpy (Etot + pV)
> and store that in the energy file for maximum accuracy.
>
> Which NPT algorithm/integrator combination is recommended that minimally
> disturbs the fluctuations?
> 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

Sounds like a great time to try the velocity verlet code with the
Martyna-Tuckerman-Tobias-Klein pressure integrator that I just
integrated into the CVS last month!   Theoretically, it should give
the correct fluctuations.

It conserves the conserved quantity correctly -- but there might be
something else subtle going on, so this would be a good test to run.

To use:
use 'md-vv' for integrator
and 'MTTK' for pcoupl.
tcoupl should remain 'Nose-Hoover'.

(Yes, I need to catch up the documentation -- I've been working on it,
but it isn't checked in yet).

Note also that 'md-vv-avek' is another integrator that uses the
average of the half step kinetic energies to determine the
temperature, instead of the full step velocities.  I'm not 100%
certain about the validity of this way of doing things this way when
combined with full step pressure control, so run 'md-vv' also if you
do 'md-vv-avek', just for comparison's sake.

Note that pV should be the volume times the applied pressure, not the
instantaneous pressure -- this was wrong a few months ago,but I posted
a correction 2-3 months ago.  Don't know what version you are using
for these calculations, so that may not be an issue anyway.