VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Sep 14 2018 - 08:44:08 CDT

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