[gmx-developers] More about the Ekin issue.

Xavier Periole x.periole at rug.nl
Thu Aug 11 20:07:40 CEST 2005

Berk Hess wrote:

> Xavier Periole wrote:
>> Berk Hess wrote:
>>> Hi,
>>> This looks like another issue, maybe your old runs encountered
>>> a bug that has since been fixed.
>>> Could you send an mdp file?
>> in attachement !
> 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.

Ok, I sorted out the problems.

1) for the small system, the reaction-field was actually gone from the 
mdp file
I used to run gmx33b. Using the tpr from gmx3.1 gives a difference of Epot
but this time it is what one would expect from the difference of T.
2) for the big system the RF for excluded atoms was responsible. Again 
the tpr from gmx3.1 give a difference but expected from the difference in T.

I'd like to get more detail about this RF correction that is included 
(or excluded)
in gmx33. could you be more precise ?


 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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