[gmx-users] Coupling groups - Thermostat
Mark.Abraham at anu.edu.au
Wed Jan 11 06:29:15 CET 2012
On 11/01/2012 4:23 PM, Tsjerk Wassenaar wrote:
> 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,
>> 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.
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
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