[gmx-developers] energies from previous step used for hamiltonian replica exchange evaluation?

[Shirts, Michael R. (mrs5pt)]

Hi, Floris-

I will check this when I can (Travelling at a conference), but the
bookkeeping in gromacs is a somewhat convoluted (on the list of things to
clean up) -- a lot of quantities are saved and not stored to file or used
immediately for various annoying reasons. So I THINK that everything is
properly accounted for.

I will take an extra look, however, when I get a chance (unless Berk gets
to it first).  I've certainly compared it to non-replica exchange, and
gotten statistical identical results -- which does not guarantee it's 100%
right, however. Note that md-vv should to the bookkeeping correctly as
well.

Best,
~~~~~~~~~~~~
Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434)-243-1821



On 6/10/14, 3:47 PM, "Floris Buelens" <floris_buelens at yahoo.com> wrote:

>Right - all the required quantities come from a single call of do_force
>before update. But the way I see it (please do correct me), as soon as
>update() is executed, all the calculated energy quantities are those from
>the previous set of coordinates, and no longer valid as the basis for a
>monte carlo move for the new state of the system.
>
>
>
>
>
>
>On Tuesday, 10 June 2014, 15:37, Berk Hess <hess at kth.se> wrote:
>Hi,
>
>Gromacs doesn't do Hamiltonian replica exchange by re-calculating
>potentials, does it?
>All potentials and lambda dependencies are calculated using the
>coordinates before update, so I don't think there is any issue at all.
>
>Cheers,
>
>Berk
>
>
>
>
>On 06/10/2014 02:56 PM, Floris Buelens wrote:
>> Hi,
>>
>> While trying to evaluate Hamiltonian replica exchange probabilities
>>'offline', e.g. not at runtime but from checkpoint files, I think I
>>might have run into an inconsistency in how they're evaluated in
>>Gromacs. My worry is that exchange probabilities are calculated at the
>>very end of the MD step loop, after update() has been called. This would
>>mean that the exchange criterion is evaluated using energies from step
>>x, but coordinates from step x+1.
>>
>> If I've got this right, the strictly correct way would be to evaluate
>>replica exchanges before update() is called, and then to recalculate the
>>energies and forces where the replica exchange attempt was successful
>>(since they were calculated according to a different U(x) and are
>>strictly no longer valid) - and only then to call update(). Or
>>equivalently to implement hybrid MC/MD, where x MD steps are followed by
>>a single MC step, where the exchange move is either accepted or rejected
>>based on a fresh energy evaluation.
>>
>> Am I missing something?
>>
>> I had a look at replica exchange probabilities between successive steps
>>and predictably the correlation is very high, but some of the deviations
>>are not so small (some sample data pasted in below).
>>
>> thanks,
>>
>> Floris
>>
>>
>>   p(n)  p(n+1)
>> 0.0080  0.0102
>> 1.0000  1.0000
>> 0.0137  0.0142
>> 0.7724  0.6141
>> 0.0418  0.0619
>> 0.0731  0.0859
>> 0.2771  0.2374
>> 0.0092  0.0130
>> 0.3064  0.2375
>> 0.0804  0.0770
>> 0.0349  0.0325
>> 1.0000  1.0000
>> 0.0506  0.0718
>> 0.1385  0.2349
>> 0.0003  0.0004
>> 0.9125  0.8968
>> 0.0000  0.0000
>> 0.7520  0.7820
>> 0.0116  0.0124
>> 1.0000  0.8525
>> 0.2255  0.2747
>> 0.0112  0.0130
>> 0.0241  0.0230
>> 1.0000  1.0000
>> 0.0015  0.0010
>> 0.0018  0.0027
>> 0.1365  0.2044
>> 1.0000  1.0000
>> 0.0104  0.0062
>> 0.0238  0.0420
>> 0.4723  0.5447
>-- 
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