[gmx-developers] Regd. potential on grid caculation in PME

[Anjan Raghunathan]

Hi Erik,
   Thanks for the suggestion. Am currently looking into gather_f_splines 
function and for more information on the code.

Anjan

Erik Lindahl wrote:

> Hi,
>
> Have a look in src/mdlib/pme.c, routine gather_f_bsplines(). The 
> potential at the points is available through the th{x/y/z} arrays, and 
> the derivative in dth{x/y/z}.
>
> It looks somewhat complicated due to the 4th order interpolation. The 
> best source of documentation on it is probably the Darden smooth PME 
> paper (Essman, 1995).
>
> Cheers,
>
> Erik
>
>
> On Nov 9, 2004, at 5:26 PM, Anjan Raghunathan wrote:
>
>> Hi Erik,
>> Thank you for the observation. Actually I would not mind having the 
>> reciprocal space potential, as could calculate direct space rather a 
>> bit tediously. And am only interested in Electrostatics so if I am 
>> not wrong I dont need the 1,4 interactions. Any suggestions on how to 
>> get the reciprocal space contribution that are calculated on the 
>> grids in pme.c?
>>
>> thanks,
>> Anjan
>>
>> Erik Lindahl wrote:
>>
>>> Hi Anjan,
>>>
>>> I don't think it will work to use the PME grid - remember that it 
>>> only contains the reciprocal space contribution to the potential, 
>>> not the direct-space part or any 1,4 contributions.
>>>
>>> Cheers,
>>>
>>> Erik
>>>
>>>
>>> On Nov 3, 2004, at 9:53 PM, Anjan Raghunathan wrote:
>>>
>>>> Hi all,
>>>> Actually I went back to the pme.c file to find where the potentials 
>>>> were being calculated. I believe they are calculated on a grid sent 
>>>> to fft with arguments nx,ny,nz. Unfortunately I am not well versed 
>>>> with fftw , so if some one could point me out to how I could use 
>>>> the grids potential calculated there to get the grids on the real 
>>>> space grid I would appreciate it.
>>>>
>>>> thanks,
>>>>
>>>> Anjan Raghunathan
>>>>
>>>> Anjan Raghunathan wrote:
>>>>
>>>>> Hi all,
>>>>> I'd like to know if there is a way of getting the
>>>>> electrostatic potentials from PME(direct+k space) in a
>>>>> plane(grid) that I define in the system every time step. I
>>>>> thought of using dummy atoms but dont know if the energy
>>>>> exclusion will take care of excluding the coulomb interactions
>>>>> also(usually get warnings like cannot exclude coulomb
>>>>> interactions.....).
>>>>> I would appreciate it if some one could point me to how
>>>>> this could be accomplished or what code could be changed to do
>>>>> this.
>>>>>
>>>>> thanks,
>>>>> Anjan Raghunathan
>>>>>
>>>>>
>>>>>
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