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.abra...@anu.edu.au
<mailto:mark.abra...@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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