[gmx-developers] More about the Ekin issue.

[Berk Hess]

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.

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.

Berk.