VMD-L Mailing List

From: Joseph Bylund (joseph.bylund_at_gmail.com)
Date: Wed Feb 01 2012 - 23:49:19 CST

John,
Thanks a bunch for answering two questions in one day (I had almost
forgotten about that previous one). Hopefully I'll have a chance to
investigate both of these in more depth later.
-Joe

On 02/02/2012 12:14 AM, John Stone wrote:
> Joe,
> This could certainly be done. You would just need to measure
> the RMSD values for each residue, and then store the results into
> one of the available per-atom data fields for each atom in the residue
> (e.g. use a "same residue as ...." type atom selection.)
> Once the data has been stored, you can use the field you've loaded the
> RMSD values into as the coloring method in VMD. For a time-varying property,
> like RMSD or RMSF you'll want to use one of the four "user" fields, since
> they are stored per-atom, for each frame.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Fri, Jan 06, 2012 at 12:40:27PM -0500, Joseph Bylund wrote:
>> I'm interested in coloring each residue in a trajectory by its RMSD to
>> its initial location. Similar to here:
>> http://www.ks.uiuc.edu/Training/Tutorials/science/aquaporin/tutorial_aqp-html/node5.html
>> (except rmsd instead of qres), but using frames of a trajectory instead of
>> aligned structures. Is there a way to do this?
>> thanks for any help,
>> -Joe 

-- 
Joseph Bylund
February 2, 2012
Strength does not come from physical capacity. It comes from an indomitable will.
Mahatma Gandhi