[gmx-users] Re: Targeted MD

[Mark Abraham]

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