David van der Spoel
spoel at xray.bmc.uu.se
Fri Oct 8 13:35:16 CEST 2004
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...
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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