[gmx-users] Coupling groups - Thermostat

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Jan 11 06:23:26 CET 2012


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.

Hope it helps,


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.


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