[gmx-users] heat exchanges

[Berk Hess]

> Date: Thu, 5 Feb 2009 10:27:13 -0500
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] heat exchanges
> 
> > The integrations errors in the electrostatics have much more effect
> > on the water than on the protein, because the water has higher charges
> > and is far more mobile. No thermostat can correct for these errors,
> > unless you use multiple groups.
> 
> I realize that it is not exactly a "thermostat", but the SD integrator  
> is expected to correct for these errors using only one temperature  
> coupling group is it not?

Yes, the SD "thermostat" has the huge advantage that it thermalizes each
degree of freedom separately.Therefore you never have incorrect temperature
distributions in your system, unless you have very serious integration
artifacts. SD also avoid any ergodicity problems.

BTW You should check your temperature for your SD runs with tau_t=1.
I often use 1, but that is with a shifted LJ potential and not with a twin-range
setup that introduces some errors. You might need to change to tau_t=0.5.
tau_t=1 has nearly no effect on the dynamics of water, whereas tau_t=0.5
slows it down somewhat. See chapter 2 of my thesis for numbers for SPC
(which diffuses twice as fast as real water):
http://dissertations.ub.rug.nl/faculties/science/2002/b.hess/

Berk



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