VMD-L Mailing List

From: Diego Gomes (diego.enry_at_gmail.com)
Date: Tue Sep 05 2023 - 13:55:55 CDT

Hi Sanjey,
could you clarify where did you get the " PorcupinePlot.tcl '' script ?

If I remember well from my GROMACs days... gmx anaeig will output a 50
frame "trajectory" for each eigenvector/eigenvalue set weighted by an
amplitude, they'll start from the same reference structure.

To see the porcupine, get the 1st and last frame of each extreme[1-2].pdb
file. 

--
Diego
On Thu, Aug 31, 2023 at 5:16 AM Sanjay Kumar Paul <
sanjaykumarpaul_at_rammohancollege.ac.in> wrote:
> While generating porcupine plot on two extreme projections...I am not
> getting results.
>
> Tk console abstract :
> loading history file ... 19 events added
> Main console display active (Tcl8.5.6 / Tk8.5.6)
> (PCAcontrol) 20 % play PorcupinePlot.tcl
> >Main< (PCAcontrol) 21 % atomselect top "name CA"
> atomselect0
> >Main< (PCAcontrol) 22 % atomselect top "name CA"
> atomselect1
> >Main< (PCAcontrol) 23 % porcupineplot::Diff atomselect1 atomselect0
> running through 494 residues
> drawing arrows for distances between 0.0 and 0.0 (colors from scheme BGR)
> done
> >Main< (PCAcontrol) 24 %
>
> The distance is showing 0.0.....thats why I think.
>
> The procedure that I have followed is as follows...
>
> gmx anaeig -v eigenvec.trr -f md_100_center.xtc -s md_100.tpr -extr
> extreme1.pdb -first 1 -last 2 -nframes 50
>
> * then I get two .pdb file - extreme11 and extreme12..each containing 50
> frames.
>
> I copied 1st frames from each to define first_frame.pdb and last_frame.pdb
>
>
> Please help me...thanks in advance
>
> Sanjay Kumar Paul
>
-- 
Diego Enry B. Gomes, PhD
Department of Physics
Leach Science Center
Auburn University
dgomes_at_auburn.edu
+1 (334) 559-4016