[gmx-users] problem with exchange probabilities in remd
Mark.Abraham at anu.edu.au
Sun Feb 24 03:34:51 CET 2008
OZGE ENGIN wrote:
> Hi all,
> I am performing a remd simulation of a peptide+water system. I have tried different temperature distributions. I am using an NVT ensemble. My temperature coupling constant is 0.1 ps.
> The problem is that upon increasing the temperature difference between the two replicas more than two (290==>294), the exchange probability decreases sharply, app. to 0.03.
Yep. That's normal for decent-sized explicit-solvent REMD. You can
choose a lowest temperature spacing that isn't an integer, of course.
> I have changed the exchange frequency in order to get a better exchange probabilities. However, it has not affected the overall exchange probabilities so much.
The frequency is independent of the probability, at least until you get
to periods so short that successive attempts are correlated. See Periole
and Mark, J Chem Phys 126 014903, and for a counter-view, Sindhikara,
Meng and Roitberg J Chem Phys 128 024103. Both frequency and probability
affect the exchange acceptance rate, of course.
> Is there anybody who has encountered such a situation?
Yep. Consider seriously how big a temperature range you might need.
There's discussion out there that the increased-sampling effect of the
increased temperature range is outweighed by the ability of the replicas
to sort themselves as a function of T. See Periole paper above. Thus,
there's no need to go to 800K, like you see implicit-solvent REMD
achieve. 373K is enough to start denaturing proteins in cooking, after
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