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From: Robin Varghese (rvarghese_at_vbi.vt.edu)
Date: Sat Feb 26 2011 - 17:37:37 CST
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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.
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