[gmx-users] Please, help me!

T.A.Wassenaar at chem.rug.nl T.A.Wassenaar at chem.rug.nl
Thu Apr 22 22:15:02 CEST 2004

Hi Akos,

You shouldn't couple just a handful of atoms seperately to a heat bath. Or
you should at least not be surprised to see large fluctuations when you
do. If you only have a few atoms, the temperature, depending on the
average speed, will fluctuate a lot. When you have more atoms, it averages
out. Moreover, coupling the temperature to a fair amount of atoms will
only involve small changes on the speeds of the atoms, whereas coupling to 
a few atoms may give considerable alterations and thus cause artefacts in 
your simulation.

The best thing to do is to merge the ions and solvent groups and couple 
this to the heat bath.



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