**From:** Andrei Tudor (*andrei.tudor.1_at_ulaval.ca*)

**Date:** Mon Aug 12 2013 - 10:40:27 CDT

**Next message:**Sijia (Scarlett) Dong: "problem with restraining a dihedral angle"**Previous message:**Sunhwan Jo: "Re: colvars and parallel-tempering with namd2.10"**In reply to:**Norman Geist: "AW: AW: vmd-l: Occupancy maps"**Next in thread:**Norman Geist: "AW: AW: vmd-l: Occupancy maps"**Reply:**Norman Geist: "AW: AW: vmd-l: Occupancy maps"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hello,

Thank you for your answers I think I understood the dx format. Just to make sure I got it, In the next header where delta is 1 for x y and z. This means that the distance between each point is 1 angstrom. So the first point (x0 y0 z0) is at origin and the second (x0 y0 z1) is at 1 angstrom from the origin along the z axis, at -54.5 -36.5 -58.7.

# Data calculated by the VMD volmap function

object 1 class gridpositions counts 113 111 110

origin -54.5 -36.5 -58.5

delta 1 0 0

delta 0 1 0

delta 0 0 1

object 2 class gridconnections counts 113 111 110

object 3 class array type double rank 0 items 1379730 data follows

0 0 0

I hope that this is right.

Andrei

________________________________________

De : owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] de la part de Norman Geist [norman.geist_at_uni-greifswald.de]

Date d'envoi : 12 août 2013 02:47

À : 'Axel Kohlmeyer'

Cc : Namd Mailing List

Objet : AW: namd-l: AW: vmd-l: Occupancy maps

Hi Axel.

Ok, now I got it. Your formerly post just contained the link to the

description of a periodic grid, therefore I thought VMD expects such a one.

Now I see it's vice versa.

Thank you.

Norman Geist.

*> -----Ursprüngliche Nachricht-----
*

*> Von: Axel Kohlmeyer [mailto:akohlmey_at_gmail.com]
*

*> Gesendet: Montag, 12. August 2013 08:15
*

*> An: Norman Geist
*

*> Cc: Andrei Tudor; Namd Mailing List
*

*> Betreff: Re: namd-l: AW: vmd-l: Occupancy maps
*

*>
*

*> On Mon, Aug 12, 2013 at 7:14 AM, Norman Geist
*

*> <norman.geist_at_uni-greifswald.de> wrote:
*

*> > Hi Andrei,
*

*> >
*

*> > I'm was working with dx files just a week ago and so already know
*

*> your
*

*> > questions. I was writing a script creating own dx files to visualize
*

*> the
*

*> > temperature distribution through the simulation cell. You can just
*

*> stay with
*

*> > the header like it is. Just put in your own origin(simply the minmax
*

*> lower
*

*> > bounds) and delta values, aswell as a title for the data at the
*

*> bottom of
*

*> > the file. The delta scaling factors usually just give the spacing
*

*> between
*

*>
*

*> the dx format as VMD reads it is described here:
*

*> http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dxplugin.html
*

*>
*

*> > the grid points. As dx is a scalar format, you do not need to save
*

*> the
*

*> > coordinates for each point in this way and so save a lot of disk
*

*> space. To
*

*> > be able to translate the grid points to cartesian coordinates again,
*

*> to
*

*> > visualize it, you need the scaling factors, which will also point to
*

*> the
*

*> > right box size if multiplied by gridsize. The delta values are
*

*> computed for
*

*> > each dimension from boxsize/gridsize. But, for some reason I didn't
*

*> > understand so far, VMD will compute the box size from
*

*> delta*(gridsize-1).
*

*>
*

*> i already explained that VMD expects a "general" and not a "periodic"
*

*> grid, i.e. the file is providing data for all corners of the described
*

*> voxels. that means for a single voxel, you need 8 (= 2x2x2) points,
*

*> for 8 (2x2x2) voxels correspondingly 27 (=3x3x3) grid points. for a
*

*> periodic data set, the values at the extremes are identical, for a
*

*> non-periodic data set, they are not.
*

*> is this so difficult to understand? where is the problem?
*

*>
*

*> axel.
*

*>
*

*> > Therefore if you create own dx file and want the "volslice" to
*

*> correctly fit
*

*> > with the box bounds and the atoms, compute the delta from
*

*> > boxsize/(gridsize-1) aswell.
*

*> >
*

*> > Im not sure if you understood the data block correctly.
*

*> >
*

*> >> 0 0 0 -> x0 y0 z0
*

*> >> 0 0 0 -> x0 y0 z1
*

*> >
*

*> > I guess you meant:
*

*> >
*

*> >> 0 -> x0 y0 z0
*

*> >> 0 -> x0 y0 z1
*

*> >
*

*> > Or:
*

*> >
*

*> >> 0 0 -> (x0 y0 z0) (x0 y0 z1)
*

*> >
*

*> > The data values will just follow each other. Every number represents
*

*> one
*

*> > gridpoint, there are no coordinates. I guess the maximum number of
*

*> points
*

*> > per line was hardcoded in VMD to five. One value per line would also
*

*> be
*

*> > possible and valid.The Z rows, as you pointed out raises 1st, then Y.
*

*> This
*

*> > means for a 2x2x2 grid, the data section would look like:
*

*> >
*

*> > 1.2 3.2 5.09 7.32 9.52 -> (x0 y0 z0) (x0 y0 z1) (x0 y1 z0)
*

*> (x0 y1
*

*> > z1) (x1 y0 z0)
*

*> > 4.8 7.2 8.4 -> (x1 y0 z1) (x1 y1 z0) (x1 y1 z1)
*

*> >
*

*> > Good luck
*

*> >
*

*> > Norman Geist.
*

*> >
*

*> >> -----Ursprüngliche Nachricht-----
*

*> >> Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im
*

*> >> Auftrag von Andrei Tudor
*

*> >> Gesendet: Freitag, 9. August 2013 18:27
*

*> >> An: vmd-l_at_ks.uiuc.edu
*

*> >> Betreff: vmd-l: Occupancy maps
*

*> >>
*

*> >> Hello,
*

*> >>
*

*> >> I am trying to understand the dx files that are made by volmap. This
*

*> is
*

*> >> what I understand until now:
*

*> >>
*

*> >> [header]
*

*> >> header info like origin etc
*

*> >> [/header]
*

*> >>
*

*> >> [data]
*

*> >> 0 0 0 -> x0 y0 z0
*

*> >> 0 0 0 -> x0 y0 z1
*

*> >> 0 0 0 -> x0 y0 z2
*

*> >> 0.001294 0 0 -> x0 y0 z3
*

*> >>
*

*> >> (...)
*

*> >>
*

*> >> 0 0 0 -> x0 y1 z0
*

*> >> 0 0 0 -> x0 y1 z1
*

*> >>
*

*> >> (...)
*

*> >>
*

*> >> [/data]
*

*> >>
*

*> >> So each row of data represents a point on the grid and they are
*

*> >> described as I have shown here.
*

*> >> This is how I understood that dx works.
*

*> >> What I didn't understand is what is represented in each point as 0 0
*

*> 0.
*

*> >> For example, on the row (0.001294 0 0) what does 0.001294 represent?
*

*> >>
*

*> >> Thank you,
*

*> >> Andrei
*

*> >
*

*> >
*

*>
*

*>
*

*>
*

*> --
*

*> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
*

*> International Centre for Theoretical Physics, Trieste. Italy.
*

**Next message:**Sijia (Scarlett) Dong: "problem with restraining a dihedral angle"**Previous message:**Sunhwan Jo: "Re: colvars and parallel-tempering with namd2.10"**In reply to:**Norman Geist: "AW: AW: vmd-l: Occupancy maps"**Next in thread:**Norman Geist: "AW: AW: vmd-l: Occupancy maps"**Reply:**Norman Geist: "AW: AW: vmd-l: Occupancy maps"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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