VMD-L Mailing List

From: Jester Itliong (jnitlion_at_mtu.edu)
Date: Sat Dec 09 2023 - 20:02:02 CST

Thank you for the clarification!

On Sat, Dec 9, 2023 at 3:48 PM Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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!4FMqOpZZmkRyK2nrJyDdX1OgdxqGeVC23eep3HKfnjVoxSXJIlo-oELQUnj_OlMy9MOPfQ0bTcdhXH7GXmA$
> College of Science & Technology, Temple University, Philadelphia PA, USA
>