[gmx-developers] More about the Ekin issue.

David van der Spoel spoel at xray.bmc.uu.se
Thu Aug 11 17:28:37 CEST 2005

> The energy difference is probably completely (except for the less than 1 
> K Ekin effect)
> due to the reaction-field correction for excluded atom pairs.
> The term is written in the log and energy file and there is an option in 
> the mdp
> file to use the old reaction-field. Using the old tpr will also cause 
> 3.3 to use the old RF.
> This term might be present in Gromos which explains the agreement.
> The term is a constant for rigid molecules and shows negligible fluctuations
> for flexible molecules. It will therefore not affect your replica exchange.
> But do you also run the REMD in NpT?
> Then you have a pV term which you probably did not account for in the 
> exchange.
> 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.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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