[gmx-users] Coupling groups - Thermostat

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jan 11 06:29:15 CET 2012

On 11/01/2012 4:23 PM, Tsjerk Wassenaar wrote:
> Hey,
> In addition to the foregoing...
> The separate coupling is to prevent draining energy from one part to 
> the other. It is pretty unlikely that either protein or tube will 
> drain the other one. Water is always a different story.
> You can check the setup you choose afterwards, like after a short run, 
> by rerunning the sinulation with the split groups and checking the 
> temperature. E.g. if you run with protein and tube in one group, the 
> should both end up having the same temperature, within the noise. Do 
> mind the noise is related to the number of atoms in a group.

Clarifying - the amount of noise is *inversely* related to the number 
atoms. That should be fairly moot, though, because a T-coupling group 
with less than a thousand atoms is probably not worth considering. The 
algorithms work best in macroscopic limits, so a group that's not at 
least 10% of your system is likely not approaching that limit - and 
grompp will warn you about that.


> Hope it helps,
> Tsjerk
>> On Jan 11, 2012 12:00 AM, "Mark Abraham" <Mark.Abraham at anu.edu.au 
>> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>> On 11/01/2012 6:52 AM, Justin A. Lemkul wrote: > > > > Steven Neumann 
>> wrote: >> >> >> >> On Tue, Jan...
>> One alternative is to pay attention to the advice at the end of 
>> section 3.4.8 of the manual and ref cited there - that separate 
>> T-coupling groups can be worse than the problems they purport to fix.
>> Mark
>> -- gmx-users mailing list gmx-users at gromacs.org 
>> <mailto:gmx-users at gromacs.org> 
>> http://lists.gromacs.org/mailman/listinfo/gmx-u...

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