Hi Dam,
Okay, I got it ... This is because in Amber11 we impose a much higher
resolution for molecular surface calculation ... which clearly changes
the numerical EPB value, i.e. the numerical algorithm should converge
better in Amber11.
Ray
On Thu, Jun 7, 2012 at 2:32 PM, Damodaran, Komath
<Komath.Damodaran.elan.com> wrote:
> Hi Qin, Ray
>
> First of all, thank you both very much for taking time to help me sorting
> this out.
>
>
>
> As Ray suggested, I set npbverb=1 in the mdin file and ran sander by hand.
> Attached are the output files. I used the same amber topology file, inpcrd
> file and a 1 frame trajectory file to generate these outputs. I have deleted
> that block of output containing the structural information since that is
> confidential and is identical in both outputs.
>
>
>
> We took a quick look at the outputs and noticed that the “residue cutoff” is
> very different (12.000 for Amber10; 99.0000 for Amber11) between the two
> versions. The Grid boundary conditions also have changed.
>
>
>
> Among other things, our main interest in migrating to Amber11 is to make use
> the energy decomposition. But we would also like to have the results
> consistent with amber10, so that we will have consistency with earlier data.
>
>
>
> If you would like to see output under different input conditions, please let
> me know. I will be more than happy to generate them.
>
>
>
> Thanks very much again,
>
> Dam
>
>
>
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Received on Thu Jun 07 2012 - 15:30:04 PDT
