Jesper,
The fine grid uses solute geometry and fine grid spacing to figure out
the solute dimension in grid unit. The program then adds a buffer,
NBUFFER grid points, to make it large enough to cover the solute.
NBUFFER can be changed, but the default, derived from twice the
diameter of the solvent probe, is large enough to cover the solute
dimension.
Ray
On Tue, Apr 16, 2013 at 10:33 AM, Jesper Sørensen <jesorensen.ucsd.edu> wrote:
> Hi Ray,
>
> Thanks for that reply. It think the statement below summed up what I was curious about and what I didn't really undestand when reading the manual.
> When you say just a bit larger, does that mean a fillratio of like 1.05 ?
>> The fine grid only depends on the solute geometry and is independent
>> of FILLRATIO. Otherwise, what's the point of using focusing? It should
>> be a just bit larger than the solute by default.
>
> Best regards,
> Jesper
>
>
> On Apr 15, 2013, at 4:54 PM, "Ray Luo, Ph.D." <ray.luo.uci.edu> wrote:
>
>> Jesper,
>>
>> So the fine grid spacing is 0.5 A, and the coarse grid spacing is 4 A.
>> NFOCUS = 2 so only these two grids are used.
>>
>> The coarse grid would be twice as large as the solute geometry since
>> FILLRATIO = 2. The grid dimension would be computed by using the 4 A
>> spacing.
>>
>> The fine grid only depends on the solute geometry and is independent
>> of FILLRATIO. Otherwise, what's the point of using focusing? It should
>> be a just bit larger than the solute by default.
>>
>> Ray
>>
>> On Mon, Apr 15, 2013 at 4:03 PM, Jesper Sørensen <jesorensen.ucsd.edu> wrote:
>>> Hi Ray,
>>>
>>> Thanks for the reply, just to clarify further...
>>> So if I specify a resolution of 0.5 (grid spacing) and a fill ratio of 2 in PBSA.in, and nfocus=2 and fscale=8. Then how does the focusing work.
>>>
>>> Is it the 2nd calculation (the focused on) that adheres to these specified parameters and then the first calculation also uses the same fill ratio and a grid spacing of 4 (0.5*8)?
>>>
>>> Best,
>>> Jesper
>>>
>>> On Apr 15, 2013, at 2:38 PM, "Ray Luo, Ph.D." <ray.luo.uci.edu> wrote:
>>>
>>>> Jesper,
>>>>
>>>> Grid spacing is the spacing gap (in Angstrom) between any two adjacent
>>>> grid points. The number of grid points per dimension apparently
>>>> depends on both the spacial dimension (in Angstrom) and the grid
>>>> spacing (in Angstrom).
>>>>
>>>> The FILLRATIO keyword controls the spacial dimension for the coarse
>>>> grid. The fine grid spacial dimension (in Angstrom) is set just a bit
>>>> larger than the solute of interest, by default. The NBUFFER keyword
>>>> can be used to customize the fine grid dimension, i.e. extra no. of
>>>> grid points to be added beyond that computed by the solute geometry
>>>> and grid spacing.
>>>>
>>>> Ray
>>>>
>>>> On Mon, Apr 15, 2013 at 2:06 PM, Jesper Sørensen <jesorensen.ucsd.edu> wrote:
>>>>> Hi all,
>>>>>
>>>>> I am trying to understand exactly what happens during a focusing calculation using PBSA.
>>>>>
>>>>> The keyword "fscale" says: Set the ratio between the coarse and fine grid spacings in an electrostatic focussing calculation. Default to 8.
>>>>>
>>>>> Does that mean that the dimensions of the grid (in angstroms) are the same, but the grid spacing on the second calculation is higher? In that case what is the advantage to not just calculating it with the higher grid spacing at the beginning? Is that calculation using the finer grid faster when better initial estimates are used from the coarser grid calculation?
>>>>>
>>>>> Or are the two calculations being done on differently sized grids, so that the fillratio is high in the first calculation, and the smaller in the second calculation?
>>>>>
>>>>>
>>>>> Best regards,
>>>>> Jesper
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Received on Tue Apr 16 2013 - 11:30:03 PDT
