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

[Mark Abraham]

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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