[gmx-users] How to add calcium ions at desired position?

[Justin A. Lemkul]

Quoting liang <petrucci123 at vip.sina.com>:

> > Never couple solvent and ions separately.  Check out:
>
> > http://wiki.gromacs.org/index.php/Thermostats
>
> > Try tc-grps = Protein Non-protein
>
> excuse me, if the system includes lipid bilayer, how should i set the
> tc-prgs?
> Protein + Lipids + Sol and Ion?
> or Protein + Non-protein ?

I think either would work, but I've personally used protein, lipids, solvent +
ions.  As long as you're not coupling a very small amount of atoms/ions to its
own bath then you should avoid problems.

-Justin

>
> thanks



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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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