[gmx-developers] More about the Ekin issue.

Xavier Periole x.periole at rug.nl
Thu Aug 11 17:35:56 CEST 2005

David van der Spoel wrote:

>>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 
>>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.
Wait ... the REMD is in NVT. The mdp file is from a Brute Force MD 
I produced to compare REMD to BFMD. BFMD are done both in NPT and NVT.
The mdp I gave and used for the comparison are NPT simulation.

I am making more test on the RF. Let you know

 Xavier Periole - Ph.D.

 Dept. of Biophysical Chemistry / MD Group   
 Univ. of Groningen
 Nijenborgh 4
 9747 AG Groningen
 The Netherlands
 Tel: +31-503634329
 Fax: +31-503634800
 email: x.periole at rug.nl
 web-page: http://md.chem.rug.nl/~periole

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