VMD-L Mailing List

From: Peter Mawanga (peter.mawanga.lagos_at_gmail.com)
Date: Fri Sep 14 2018 - 10:55:42 CDT

Thanks Giacomo

I understood that the three values do not correspond to the x, y and z
values of a 3D coordinate.

But I am not sure about the meaning of this particular line (present in the
link given earlier):

"Grid data follows, with three values per line, ordered z fast, y
medium, and x slow."

Does this statement imply the grid values are arranged as:

(Using a 2 x 2 x 2 grid as an example)

////////////////////////////

x1 y1 z1 gridvalue1
x1 y1 z2 gridvalue2
x1 y2 z1 gridvalue3
x1 y2 z2 gridvalue4
x2 y1 z1 gridvalue5
x2 y1 z2 gridvalue6
x2 y2 z1 gridvalue7
x2 y2 z2 gridvalue8

////////////////////////////

OR

////////////////////////////

z1 y1 x1 gridvalue1
z1 y1 x2 gridvalue2
z1 y2 x1 gridvalue3
z1 y2 x2 gridvalue4
z2 y1 x1 gridvalue5
z2 y1 x2 gridvalue6
z2 y2 x1 gridvalue7
z2 y2 x2 gridvalue8

////////////////////////////

Or something else altogether? Please let me know.

On Fri, Sep 14, 2018 at 7:14 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> The link you pasted documents the file reader routine for .dx files, and
> the expected format. Just re-read it carefully and things should be clear.
>
> One only thing that you should be aware of is that the limit of three
> values per line are not related to x, y, z: they are written this way
> simply to avoid long lines.
>
> If you are still unsure, try creating a .dx file with what you think is
> the syntax (a 2x2x2 or a 3x2x2 grid should be enough), and see if it works
> as expected.
>
> Giacomo
>
> On Fri, Sep 14, 2018 at 6:03 AM Peter Mawanga <
> peter.mawanga.lagos_at_gmail.com> wrote:
>
>> Dear VMD users
>>
>> Upon doing electrostatics calculation using "PME Electrostatics" plugin
>> in VMD, a ".dx" file is generated with the following output:
>>
>> ////////////////////////////
>>
>> # PME potential (kT/e, T=300K)
>> object 1 class gridpositions counts 100 100 100
>> origin 0.5 0.5 0.5
>> delta 1 0 0
>> delta -0 1 0
>> delta -0 -0 1
>> object 2 class gridconnections counts 100 100 100
>> object 3 class array type double rank 0 items 1000000 data follows
>> -72.1699 -71.4829 -70.5591
>> -69.4607 -68.2532 -66.9999
>> -65.7542 -64.5533 -63.4164
>> -62.3467 -61.3386 -60.385
>> -59.4842 -58.6428 -57.8751
>>
>> ////////////////////////////
>>
>> I am not sure how these grid values are arranged as such. Although the
>> following link suggests that these are arranged in the format below:
>>
>> https://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dxplugin.html
>>
>> ////////////////////////////
>>
>> x1 y1 z1 value1
>> x1 y1 z2 value2
>> x1 y2 z1 value3
>> x1 y2 z2 value4
>> x2 y1 z1 value5
>> x2 y1 z2 value6
>> x2 y2 z1 value7
>> x2 y2 z2 value8
>>
>> ////////////////////////////
>>
>> Please let me know if I am correct or the format is different?
>>
>> --
>> Cheers
>> Peter
>>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
> 

-- 
Cheers
Peter