Hi,
Many thanks for your prompt reply. Now, after going through the description
of bonded and non-bonded models in the tutorial page, I am a little
confused about the model I should choose. The tutorial says about the
bonded model that -
' While ligand exchange of coordination number (CN) switching process
certainly do happen in protein metal sites, these occur on much slower
timescales than what is observed for metal ions in aqueous solution.
.......... Since typical MD simulation timescales are at the nanosecond or
microsecond levels (circa 2014), the bonded model is an effective approach
to study processes where ligand exchange does not occur over the timescales
employed.'
Though the Mn2+ ion in my protein do suggested to have CN switching during
the catalysis, I am aiming for only about 100ns simulation to find out the
role of some water molecules in the ligand-ion interaction. So I just
wonder which model will be best fit in my case.
Any suggestions would be very much appreciated.
Thanks
Anu
On Tue, Jan 26, 2016 at 10:09 PM, Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> Hi Anu,
>
> The 12-6 LJ model is easier to use than the 12-6-4 LJ-type model and could
> make your simulation faster, since AMBER only supports 12-6-4 simulation in
> the cpu version but supports 12-6 simulation in both cpu and gpu version.
> If you are using cpus to run AMBER and want to get more accurate results,
> the 12-6-4 LJ model is reommended.
>
> Hope it helps,
> Pengfei
>
> > On Jan 26, 2016, at 11:34 AM, anu chandra <anu80125.gmail.com> wrote:
> >
> > Dear Amber users,
> >
> > The protein I am working with have a Mn2+ ion at its active site. The ion
> > suspected to form coordination bond with neighboring residues and these
> > bonds will break and re-form during the course the reaction. As read from
> > the tutorial page, I suppose I should use the non-bonded model. But, I
> just
> > wonder which of the non-bonded model ( 12-6 Lj or 12-6-4 Lj) better suite
> > in my case.
> >
> > Any help would be very much appreciated.
> >
> > Many thanks
> >
> > Anu
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>
>
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Received on Tue Jan 26 2016 - 12:00:03 PST
