[gmx-users] Re: Targeted MD

Novice xwxnju at gmail.com
Thu Jan 10 06:45:26 CET 2008

Thanks a lot for the detailed and nice explainations.

2008/1/10, Mark Abraham <Mark.Abraham at anu.edu.au>:
> wei-xin xu wrote:
> > Some hints on practices that generally *not a good idea* to use:
> >
> >     * Do not use separate thermostats for different components of your
> >       system. Some molecular dynamics thermostats only work well in the
> >       thermodynamic limit. If you use one thermostat for, say, a small
> >       molecule, another for protein, and another for water, you are
> >       likely introducing errors and artifacts that are hard to predict.
> >       In particular, do not couple ions in aqueous solvent differently
> >       from that
> >     * solvent.
> >
> > Sorry that I do not actually understand here. The link I copied above
> > shows that better not to "couple ions in aqueous solvent differently
> > from that solvent". Maybe not separately but differently (mean different
> > temperature)?
> "differently" is intended to mean "in a separate group". I'll reword my
> wiki sentence.
> The original poster showed an .mdp file where
> tc-grps = Protein ; SOL CL UNK
> (or something like that). Now actually, the semicolon starts a comment,
> so he's only thermostatting the protein. That's a bad idea because it
> will lead to net heat flow from the protein to the rest of the system.
> Even if there were no semicolon, there are probably a few thousand
> solvent molecules and a handful of chloride ions. Temperature is defined
> from the average kinetic energy, and the average kinetic energy of a
> handful of ions in thermal contact with many other atoms will have large
> fluctuations, and this will lead to the thermostat doing lots of
> corrections, for lots of heat flow in and out of the system. So treating
> solvent+ions+other_small_stuff as one group for T-coupling purposes is a
> good idea, and the standard group "Non-Protein" serves well here. So a
> usual tc-grps line has "Protein Non-Protein" for a protein simulation.
> Mark
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