[gmx-users] counterions

Xavier Periole x.periole at chem.rug.nl
Fri Oct 8 14:17:02 CEST 2004

David van der Spoel wrote:

>On Fri, 2004-10-08 at 12:20, Xavier Periole wrote:
>>Osmany Guirola Cruz wrote:
>>>In last mail i forget do a question... and it's relative to counterions....
>>>Where can i find information about the role of counterions in MD..
>>>Should i have to use counterions in all my simulations or depend if i use PME 
>>>in my simulation or another thing?
>>If I remember your input file correctly you defined three groups for the
>>Temperature coupling : Protein Sol Cl-
>>I would advise to put the Sol and Cl- in the same bath !!! You more likely
>>do not have enought Cl- to isolate them in a separate bath without having
>>enormous fluctuations.
>Wouldn't there be enormous fluctuations anyway? Just you don't see them
>in the bath... Of course you disturb the system less when you have a
>larger bath, so your recommendation is good. But if you were to measure
>the temperature of a single Cl- in water it would fluctuate a lot...
You are right. Although I am quite convinced that the fluctuation would 
much higher
when simulated with two baths, which would result in a constant scaling 
of their velocities
and so modificatin of the dynamics of the system ... so perturbation as 
you mentioned.
Just to evaluate the diference I just sent two jobs of pure water where 
in one of them
one water molecule is isolated from the others. Could be interesting to 
have an idea of
the difference.



   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 chem.rug.nl
   web-page: http://md.chem.rug.nl/~periole

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