Dam,
Nothing else would change the numerical value this much ... basically
the solvent accessible arc dot is generated at the resolution of 1/16
A instead of 1/4 A as shown in the output files. Thus the molecular
surface reentrant portion is rendered much better (smoother) in Amber
11. This leads to different dielectric constant mappings between
Amber10 and Amber11, so different electrostatic solvation free
energies.
That was also why Amber11 uses more memory and is a bit slower than
Amber10 for mmpbsa calculations.
However, in Amber12 Qin has improved the algorithm, the numerical
value is closer to that by Amber11 but its efficiency (memory/speed)
is closer to Amber10.
All the best,
Ray
On Thu, Jun 7, 2012 at 3:18 PM, Damodaran, Komath
<Komath.Damodaran.elan.com> wrote:
> Hi Ray,
> Is that it? What about the other parameters, residue cutoff and Grid boundary conditions that look different in the two outputs? BTW, could you please explain what they are?
>
> Thanks!
> Dam
>
> -----Original Message-----
> From: rayhuangluo.gmail.com [mailto:rayhuangluo.gmail.com] On Behalf Of Ray Luo, Ph.D.
> Sent: Thursday, June 07, 2012 3:02 PM
> To: Damodaran, Komath
> Cc: AMBER Mailing List; Qin Cai
> Subject: Re: [AMBER] Sander MMPBSA (EPB) Differences between Amber10 and Amber11
>
> 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 - 17:00:03 PDT
