Hi George,
There is no smoothing function with PME - PME itself 'could' be considered
the smoothing function. Essentially the cutoff just divides up
electrostatics between direct and reciprocal space and so the concept of
cut off is not really the correct name to use here. I would suggest
reading up on Ewald and PME and then hopefully all will become clear.
All the best
Ross
On 4/16/13 1:02 PM, "George Tzotzos" <gtzotzos.me.com> wrote:
>Thank you Jason,
>
>I have an additional question. Using cut=8.0 implies a cutoff distance of
>8 Angstrom for non-bonded interactions using PME. Is there any smoothing
>performed? If yes, how?
>
>Best regards
>
>George
>
>On 16 Apr 2013, at 21:07, Jason Swails <jason.swails.gmail.com> wrote:
>
>> On Tue, Apr 16, 2013 at 2:24 PM, George Tzotzos <gtzotzos.me.com> wrote:
>>
>>> The Amber 11 manual, p.19 states
>>> "Non-additive" force fields based on atom-centered dipole
>>>polarizabilities
>>> can also be used. These add a "polarization" termŠetc"
>>>
>>> I assume that sander by default does not use such polarisation term.
>>>
>>> Can anyone please confirm that this is the case?
>>>
>>
>> This is correct. This is specified in the topology file now.
>>
>> All the best,
>> Jason
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
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>
>
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Received on Tue Apr 16 2013 - 13:30:03 PDT
