[gmx-users] Zn moves away from protein - ligand complex

[HongTham]

Hi Mark,
I got you now. Thanks for your kind reply.
Best wish :D
Hongtham

On Wed, Apr 20, 2016 at 4:19 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> You've already said you know the ion isn't diffusing out, so there can be
> no simulation problem.
>
> You'd have the same kind of visualisation problem if the default protein
> index group didn't exist and instead each residue was its own group. Then
> they would each be handled separately, and thus not necessarily
> consistently with each other. If you want a whole assembly treated
> together, you have to ask for it explicitly. The protein has a default
> index group to do that, because people normally want that. Currently only
> you know that this ion is special, so the computer can't know that you
> care...
>
> Mark
>
> On Tue, 19 Apr 2016 04:13 HongTham <hongtham0709 at gmail.com> wrote:
>
> > Hi Mark,
> > Sorry that I don't get you. Can you explain a little bit for me? I just
> > wonder if Zn really moves out of active site, when I display multi box in
> > VMD, there shouldn't have another Zn bound in there.
> > Sincerely,
> > Hongtham
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