[gmx-users] Coupling groups - Thermostat

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Jan 11 10:16:46 CET 2012

Hi Mark,

Please, I did not state that the groups should be coupled separately.
I suggested checking the temperatures of the subgroups of a combined
T-coupling group. So 'moot ..., because T-coupling group ...' is not
really in place.



On Wed, Jan 11, 2012 at 6:29 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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.
> Mark
> Hope it helps,
> Tsjerk
> On Jan 11, 2012 12:00 AM, "Mark Abraham" <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
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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