VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Dec 09 2023 - 14:48:21 CST

There is no special meaning in having three values per line. Each value is
a different value for the computed potential.
There could be 6 or 9 or 10 or whatever number of items per line.
The location in x, y, and z is determined by the grid defined by xorg +
ix*xdel, yorg + iy*ydel, zorg + iz*zdel.
The data points start at ix, iy, iz = (0, 0, 0) and then the second point
is (0, 0, 1), the third is (0, 0, 2) and so on until (0, 0, nz).
The next point is for (0, 1, 0) and then (0, 1, 1) and so on. The last
point is the property value for (nx, ny, nz).

On Sat, Dec 9, 2023 at 1:23 PM Jester Itliong <jnitlion_at_mtu.edu> wrote:

> Hello.
>
> I have been trying to understand the .dx file output from the PME
> Electrostatics Analysis plugin. I found this guide
> https://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dxplugin.html to
> make sense of the file format but I have been having a hard time
> understanding the grid data or the three data values per line, namely
> ordered z fast, y medium, and x slow. I understand that these data are the
> electrostatic potential values in units of kT/e but I guess I don't
> understand why there are three values of this potential. Can someone help
> me make sense of this?
>
> As a background information, I wanted to analyze the values in this file
> to know whether the sum of the potentials is ~0 so I wanted to make sure
> that I am extracting the appropriate data correctly. Thank you in advance
> for your help.
>
> -Jester
>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!7giwjjN5PK3PbTfpAY-p2NjWH4JSu5ePTyekK1U9AgPB_-3JVMWxl4UHwU5HRdYfliunnnbGYZPJfKx4Dw$ 
College of Science & Technology, Temple University, Philadelphia PA, USA