On 11/01/2012 8:16 PM, Tsjerk Wassenaar wrote:
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.
Right, sorry. I thought you were suggesting comparing two different
coupling regimes. You weren't.
Mark
Cheers,
Tsjerk
On Wed, Jan 11, 2012 at 6:29 AM, Mark Abraham<mark.abra...@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.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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