VMD-L Mailing List

From: Robin Varghese (rvarghese_at_vbi.vt.edu)
Date: Sat Feb 26 2011 - 17:18:56 CST

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?

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.