VMD-L Mailing List

From: Ebert Maximilian (m.ebert_at_umontreal.ca)
Date: Tue Oct 06 2015 - 14:38:43 CDT

Hi,

Thank you Arash and Axel I finally understood. For other people with difficulties here is a really simple scheme. Your data looks like this:

# Data from VMD
# created by volutil, T = -1.00 Kelvin,
object 1 class gridpositions counts 55 54 56
origin 13.5 22.5 13.5
delta 1 0 0
delta 0 1 0
delta 0 0 1
object 2 class gridconnections counts 55 54 56
object 3 class array type double rank 0 items 166320 data follows
3.59969 3.74529 3.63887
3.50111 3.1404 3.5214
3.61568 3.39755 3.97473

Energy values start with 3.59969. So for the coordinates:

(0 0 0) value 3.599690
(0 0 1) value 3.745290
(0 0 2) value 3.638870
(0 0 3) value 3.501110
…
(0 0 55) value 3.893990
(0 1 0) value 3.745290
(0 1 1) value 3.638870
(0 1 2) value 3.501110
…
(0 53 55) value 4.213390
(1 0 0) value 3.745290
(1 0 1) value 3.638870
…
(54 53 53) value 3.156120
(54 53 54) value 3.388900
(54 53 55) value 3.448940

And as side note. To get from the ILS output to the kj/mol we just have to do:

Value * kb (Boltzmann constant) * T * Na (Avogadro's number) / 1000

Maybe this will help others as well.

Thanks again
Max

On Oct 6, 2015, at 1:47 AM, Ebert Maximilian <m.ebert_at_umontreal.ca<mailto:m.ebert_at_umontreal.ca>> wrote:

________________________________
From: Arash Azari
Sent: Tuesday, October 06, 2015 1:47:38 AM (UTC-05:00) Eastern Time (US & Canada)
To: vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>
Cc: Ebert Maximilian
Subject: Re: vmd-l: OpenDX file format website down: What do the three values at each grid point represent

Hi,

Here you can find more information on DX format which clarifies Axel's comment.
http://www.poissonboltzmann.org/docs/file-format-info/

Best regards,
Arash

On Mon, Oct 5, 2015 at 5:57 PM, Axel Kohlmeyer <akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com><mailto:akohlmey_at_gmail.com>> wrote:

On Mon, Oct 5, 2015 at 11:05 AM, Ebert Maximilian <m.ebert_at_umontreal.ca<mailto:m.ebert_at_umontreal.ca><mailto:m.ebert_at_umontreal.ca>> wrote:
Thanks Axel for your clarification. So what are those 3 values/properties calculated at each grid point. I now that each line represents a certain

​you didn't read my email properly. there are not 3 values per point, but *one* value per grid point, representing whatever property that you have computed at the location of that grid point or representing the voxel. as i already mentioned, the fact that you have 3 numbers per line has *NO* significance at all. count the number of lines/points and compare to the number of grid points that you *should* have as indicated in the header of the dx file. it will only work, if you have one data element per grid point. the dx format makes no distinction between a blank and a newline.

place/grid point in my system. So the 3D coordinate is taken by the row and the information about origin and grid size. But the three values/properties computed what are they? How can I imagine it? having for instance grid point 0,0,0 having value 85,75,15. What is the meaning of 85, 75 and 15 and position 0,0,0?

​such grid maps are usually visualized as isosurfaces or colormaps projected on a cut plane through the ​volume.

axel.

Thank you

On Oct 2, 2015, at 2:09 PM, Ebert Maximilian <m.ebert_at_umontreal.ca<mailto:m.ebert_at_umontreal.ca><mailto:m.ebert_at_umontreal.ca>> wrote:

________________________________
From: Axel Kohlmeyer
Sent: Friday, October 02, 2015 2:09:36 PM (UTC-05:00) Eastern Time (US & Canada)
To: Ebert Maximilian
Cc: <vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu><mailto:vmd-l_at_ks.uiuc.edu>>
Subject: Re: vmd-l: OpenDX file format website down: What do the three values at each grid point represent

On Fri, Oct 2, 2015 at 1:36 PM, Ebert Maximilian <m.ebert_at_umontreal.ca<mailto:m.ebert_at_umontreal.ca><mailto:m.ebert_at_umontreal.ca><mailto:m.ebert_at_umontreal.ca<mailto:m.ebert_at_umontreal.ca>>> wrote:
Hi there,

unfortunately most references to the opendx file format are down. could anyone elaborate on the meaning of the three values in the dx output of the ILS calculation. What do they represent for each grid point?

the fact that there are 3 numbers in a line has no relevance at all.

*all* of those numbers are the value of the computed property at a given location in a regular grid.
the grid itself is defined by the three grid vectors and the counts, thus the location of the individual grid points has to be inferred from that and the location of the origin.

axel

Thank you very much,

Max

PS: I saw http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dxplugin.html and it is not clear to me 

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com><mailto:akohlmey_at_gmail.com><mailto:akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com>>  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.
--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com><mailto:akohlmey_at_gmail.com>  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.
--
Arash Azari