[gmx-users] issue in replica exchange

[XAvier Periole]

Some good news … 

The tpr files provided by Simone do NOT show abnormal behaviour! This good news :)) 

However after turning ON the particle decomposition option to mdrun (-pd) I got a warnings of water not being able to be settled and a crash. This was still with Simone's trips … I took that as a good sign! 

Then I went back to my system and changed the topology to be able to turn OFF the particle decomposition that I need to use due to a "long" bond … the system when right trough 650 ps with many exchanges without a complain. I would have to check the continuity in the energies, Temp and other but it seems to be quite clear:

The problem I am facing is located in the particle decomposition section of the code. 

I will fill a redmine and let see how to proceed from there. I won't be able to do this before middle of next week though.

Tks for your help,
XAvier.


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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