[gmx-users] Positive and negative ions move in the same direction under a constant electric field?

[Tom Weingarten]

I'm not sure if this has been addressed previously, but perhaps the reason
why we're seeing so many users performing incorrect temperature coupling of
ions is because that is how it is done in the very popular fwspider
tutorial. In fact this tutorial is the first hit on google for "gromacs
tutorial."

; Berendsen temperature coupling is on in three groups
Tcoupl              =  berendsen
tau_t               =  0.1          0.1  0.1
tc_grps             =  protein      sol  CL­
ref_t               =  300          300  300

http://www.google.com/url?sa=t&ct=res&cd=1&url=http%3A%2F%2Fwww2.umdnj.edu%2F~kerrigje%2Fpdf_files%2Ffwspidr_tutor.pdf&ei=wuZBRpz3IZDOwQKZqaT5DQ&usg=AFrqEzdUTsDP3qQxqY90ZIlZ2PrpLg8FXg&sig2=3IIJaY71ZM6wMwWtUAE5AA

Hopefully this is useful, my apologies if I'm not understanding the issue
correctly.

,Tom

On 5/7/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>
> 林揚善 wrote:
> > tc_grps           =    SOL     NA+    CL-
> >
> > tau_t               =    0.1      0.1      0.1
> >
> > ref_t               =    300      300     300
>
> I don't know if it's germane to your problem, but this is about the
> tenth time this month that someone has reported an .mdp file with groups
> of ions coupled independently to thermal baths. This is a Bad Idea, and
> means that even if everything else is working correctly, your simulation
> isn't as close to accurate as you would want. Search the mailing list
> for reasons why.
>
> Mark
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