[gmx-users] issue in replica exchange

[Michael Shirts]

Summarizing!

On Fri, May 3, 2013 at 12:31 AM, XAvier Periole <x.periole at rug.nl> wrote:
>
> Are confirming that you reproduce the problem with gmx-4.6.1 or simply summarizing in case we lose track :))
>
> On May 2, 2013, at 23:31, Michael Shirts <mrshirts at gmail.com> wrote:
>
>> So to summarize -- the problem appears to be with particle decomposition.
>>
>> On Thu, May 2, 2013 at 4:15 PM, XAvier Periole <x.periole at rug.nl> wrote:
>>>
>>> I'll look at the 4.6.1 version next week, I could install it but I got a conflict between the environmental variable defining openMP variable but I turned it off during compilation …
>>>
>>> You could try to run on particle decomposition to see if you get a problem … it should one quite quick.
>>>
>>> On May 2, 2013, at 2:36 PM, Michael Shirts <mrshirts at gmail.com> wrote:
>>>
>>>> Both.  So if 4.6.1 doesn't work, I want to know so we can patch it
>>>> before 4.6.2 comes out.  If it does work, then there is probably stuff
>>>> that can be backported.
>>>>
>>>> On Thu, May 2, 2013 at 8:32 AM, XAvier Periole <x.periole at rug.nl> wrote:
>>>>>
>>>>> You mean working with or working on the code?
>>>>>
>>>>> I'll try gmx-4.6.1
>>>>>
>>>>> On May 2, 2013, at 2:26 PM, Michael Shirts <mrshirts at gmail.com> wrote:
>>>>>
>>>>>> Quick check here -- is 4.6 behaving correctly?  I actually spent some
>>>>>> time working on REMD in 4.6, and it seems to be behaving  correctly in
>>>>>> my hands with temperature and pressure control.
>>>>>>
>>>>>> Thanks for any additional info on this!
>>>>>>
>>>>>> On Thu, May 2, 2013 at 8:18 AM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>>>>>>> On Thu, May 2, 2013 at 12:58 PM, XAvier Periole <x.periole at rug.nl> wrote:
>>>>>>>
>>>>>>>>
>>>>>>>> I saw that redmine report, which could be related but it seems to happen
>>>>>>>> only for runs done outside the domain and particle decompositions.
>>>>>>>>
>>>>>>>> I'll fill up a red mine.
>>>>>>>>
>>>>>>>> Anything I could do to help speeding the fix?
>>>>>>>
>>>>>>> What'd be really nice is some thought on how one can demonstrate that the
>>>>>>> implementation of the exchange matches what would be expected from the
>>>>>>> theory. For T-exchange under NVT, it is sufficient to rescale velocities
>>>>>>> and quantities derived from them by the correct factor. That includes
>>>>>>> various things like T-coupling history and integrator half-step quantities
>>>>>>> (and does REMD with leap-frog make sense anyway?). For NPT, there's
>>>>>>> probably also some P-coupling quantities to scale, and the box to exchange.
>>>>>>> Anything I've missed? Hopefully virial contributions don't matter either
>>>>>>> way?
>>>>>>>
>>>>>>> Perhaps a decent first step is to hack the code to do a "self exchange," by
>>>>>>> clearing the entire state and rebuilding with what would/should be received
>>>>>>> from an exchange with a hypothethetical replica in an identical
>>>>>>> pre-exchange state. Only if the code can do that (i.e. mdrun -reprod
>>>>>>> produces a trajectory indistinguishable from a run that does not attempt
>>>>>>> this self exchange) is it worth considering proper state exchanges, and the
>>>>>>> process of making the code do the former should illustrate what is required
>>>>>>> for the latter.
>>>>>>>
>>>>>>> Mark
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