[gmx-developers] More about the Ekin issue.

Berk Hess hessb at mpip-mainz.mpg.de
Thu Aug 11 17:37:30 CEST 2005

>>But do you also run the REMD in NpT?
>>Then you have a pV term which you probably did not account for in the 
>>If you do account for the pV term it is around 10x as larger as the 
>>energy difference
>>and will therefore ruin the efficiency (and maybe accuracy) of your REMD.
>According to Xavier's mdp file he does use NPT simulation, the question
>is which REMD he uses... 
>I'm not sure whether including the pV term is bad, it make the
>acceptance ratio go to 40%, but the overall number of exchanges also
>depends on the frequency with which you try to exchange. The guys that
>make all these algorithms don't usually test it on proteins, but on
>simple model systems.
The acceptance ratio does not say anything about efficiency.
The pV term is roughly 10x larger the energy term, so the energy difference
has a negligible influence on the exchange probability.
The exchange probability is almost fully determined by pV.
Fluctuations in the solvent probably contribute most to pV.
So you just exchange based on fluctuations in the solvent
and not on the conformation of the solute.
I have no idea how efficient REMD based (mainly) on the pV criterion is.

Another issue is that the pV distribution with Berendsen pressure
coupling is quite off for small systems. For 400 waters:
Berendsen: pV RMSD 375 kJ/mol
Parrinello-Rahman: pV RMSD 490 kJ/mol


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