[gmx-users] Coupling groups - Thermostat
Mark.Abraham at anu.edu.au
Wed Jan 11 12:05:33 CET 2012
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.
> 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:
>> 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
>> 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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