[gmx-users] issue in replica exchange
x.periole at rug.nl
Thu May 2 14:32:58 CEST 2013
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
>> 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.
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