[gmx-users] problem with exchange probabilities in remd
OZENGIN at KU.EDU.TR
Sun Feb 24 12:48:21 CET 2008
Thank you for your suggestions Mark and David.
I have read papers you mentioned. Moreover, I also read the Berk Hess's paper in which the NPT & NVT remd was compared (JMB 354/173-183).
Since I have not a high T within my temperature distribution (the highest one is around 320K), there will be no large pressure input. In Berk's paper, it was stated that the fluctuation in volume is negligible in NPT simulation. However, due to the low density value at high T, the energy of the system will be high leading to a decrease in the overlapping of energy distribution as well as the exchange probabilities.
I am looking forward to the implementation of NVT within the temperature generator :-)
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Sun, 24 Feb 2008 13:34:51 +1100
Subject: Re: [gmx-users] problem with exchange probabilities in remd
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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