VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Feb 27 2011 - 22:54:11 CST

Hi,
  Your question wasn't entirely clear to me, but if you're asking how
you can determine which grid point is closest to a given atom, this is
some simple 3-D geometry calculation.

The small subset of the OpenDX file format emitted by
APBS (and read by VMD) is summarized briefly here:
  http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dxplugin.html

Much more detailed documentation on the full OpenDX file
format is available here:
  http://opendx.informatics.jax.org/docs/html/pages/usrgu067.htm#HDRIMD

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Feb 26, 2011 at 06:37:37PM -0500, Robin Varghese wrote:
>
> Sorry, I haven't used a mailing list before.
>
> 1. How can I map the numbers from the pot.dx file onto particular atoms?
>
> Thank you for your time and comments/suggestions.
> Robin
>
> ----- Original Message -----
> From: "Axel Kohlmeyer" <akohlmey_at_gmail.com>
> To: "Robin Varghese" <rvarghese_at_vbi.vt.edu>
> Cc: vmd-l_at_ks.uiuc.edu
> Sent: Saturday, February 26, 2011 6:29:50 PM
> Subject: Re: vmd-l: Pot.dx files
>
> On Sat, Feb 26, 2011 at 6:18 PM, Robin Varghese <rvarghese_at_vbi.vt.edu> wrote:
> > Axel,
> >
> > I am going to try some more runs on VMD and then can I   get back to you and the mailing list.  Can I email back later tonight and/or Sunday?
>
> you can always post to the list and hope that somebody
> has time to reply, even if i am not around. there are a lot of
> people subscribed to this list and many of them can give
> very qualified answers, if you articulate your problem well.
>
> please note, that the list processing adds some lag time
> until you see a reply (or your post) and also that people
> live in very different time zones.
>
> axel.
>
> > Thank you for your help!
> >
> > ----- Original Message -----
> > From: "Axel Kohlmeyer" <akohlmey_at_gmail.com>
> > To: "Robin Varghese" <rvarghese_at_vbi.vt.edu>
> > Sent: Saturday, February 26, 2011 6:05:25 PM
> > Subject: Re: vmd-l: Pot.dx files
> >
> > robin,
> >
> > please always copy the mailing list.
> >
> > On Sat, Feb 26, 2011 at 5:50 PM, Robin Varghese <rvarghese_at_vbi.vt.edu> wrote:
> >> Hey Axel,
> >>
> >> I just saw your email and thank you for replying to my question.  I am a novice in VMD as you can see and  I really appreciate your help.
> >
> > the problem you are describing has very little to do with VMD.
> >
> >> I ran a polymer (10-mer DNA MD generalized born,inifinite cut off) and took snapshots once in the initial stages and once in the end stage.  After running through VMD(APBS) I visually looked at the snapshots of the simulation. I compared the two pictures qualitatively (visually) and concluded that there was not much difference in the charges in both instances. I need to save a potential distrubution which gives me potential values in each surface vertex point.  Then I wanted to compare the average of the 10 largest and 10 smallest values of each snapshot.  This way I can qualitatively compare the electrostatic surface potential ofr the first and last snapshot.
> >
> > a few comments:
> >
> > - you don't see much changes, because you leave out the water.
> >  ... and what about counter charges?
> >
> > - DNA is a rather rigid structure
> >
> > - a molecular surface is an ill-defined object. you have highly
> > condensed atom cores
> >  with very diluted and very soft electrons around them. how will you
> > define where
> >  the molecule ends and the vacuum begins.
> >
> > - after you have your 10 numbers, what do they tell you?
> >
> > axel.
> >
> >> Thanks,Robin
> >>
> >> ----- Original Message -----
> >> From: "Axel Kohlmeyer" <akohlmey_at_gmail.com>
> >> To: "Robin Varghese" <rvarghese_at_vbi.vt.edu>
> >> Cc: vmd-l_at_ks.uiuc.edu
> >> Sent: Saturday, February 26, 2011 4:50:57 PM
> >> Subject: Re: vmd-l: Pot.dx files
> >>
> >> On Sat, Feb 26, 2011 at 4:02 PM, Robin Varghese <rvarghese_at_vbi.vt.edu> wrote:
> >>> Hello,
> >>> I have a pot.dx file from running APPBS through VMD.  When I open the pot.dx file through my text editor I see three columns.  What do each column of numbers represent.  I am trying to compute the electrostatic surface potential.  Can you please help?
> >>
> >> robin,
> >>
> >> the fact that you see three columns has no relevance. it could be five
> >> or ten and it
> >> would not change anything.  each number is the value of the
> >> electrostatic potential
> >> in space at a grid point that is described through the grid
> >> description in the header.
> >> it basically tells you how the data on a multi-dimensional grid is
> >> mapped to a one
> >> dimensional list.
> >>
> >> here is the blurb from the dx file reader in VMD that may be helpful:
> >>
> >> /* DX potential maps
> >>  *
> >>  * Format of the file is:
> >>  * # Comments
> >>  * .
> >>  * .
> >>  * .
> >>  * object 1 class gridpositions counts xn yn zn
> >>  * origin xorg yorg zorg
> >>  * delta xdel 0 0
> >>  * delta 0 ydel 0
> >>  * delta 0 0 zdel
> >>  * object 2 class gridconnections counts xn yn zn
> >>  * object 3 class array type double rank 0 items { xn*yn*zn } [binary]
> >> data follows
> >>  * f1 f2 f3
> >>  * f4 f5 f6 f7 f8 f9
> >>  * .
> >>  * .
> >>  * .
> >>  * object "Dataset name" class field
> >>
> >>  * Where xn, yn, and zn are the number of data points along each axis;
> >>  * xorg, yorg, and zorg is the origin of the grid, assumed to be in angstroms;
> >>  * xdel, ydel, and zdel are the scaling factors to convert grid units to
> >>  * angstroms.
> >>  *
> >>  * Grid data follows, with a single or multiple values per line (maximum
> >>  * allowed linelength is hardcoded into the plugin with ~2000 chars),
> >>  * ordered z fast, y medium, and x slow.
> >>  *
> >>  */
> >>
> >> "electrostatic surface potential" is a very vague description in this context.
> >> what kind of surface, where. and how do you determine the surface?
> >> the more precise you describe your problem and why you want to compute
> >> what, the easier it is for other people to help.
> >>
> >> axel.
> >>
> >>> Thanks,
> >>> Robin
> >>>
> >>
> >>
> >>
> >> --
> >> Dr. Axel Kohlmeyer
> >> akohlmey_at_gmail.com  http://goo.gl/1wk0
> >>
> >> Institute for Computational Molecular Science
> >> Temple University, Philadelphia PA, USA.
> >>
> >
> >
> >
> > --
> > Dr. Axel Kohlmeyer
> > akohlmey_at_gmail.com  http://goo.gl/1wk0
> >
> > Institute for Computational Molecular Science
> > Temple University, Philadelphia PA, USA.
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com  http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078