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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Received on Tue Jan 26 2016 - 09:00:04 PST
