VMD-L Mailing List

From: Eduard Schreiner (eduard.schreiner_at_rub.de)
Date: Mon Aug 21 2006 - 12:09:34 CDT

On Monday 21 August 2006 15:26, Ivan Degtyarenko wrote:
>
> Dear All, if someone has any experience and could share it, I'd really
> appreciate. I'm in process of analyzing the molecular dynamics trajectory,
> the ion solvated in water, and may be somebody has ready solutions, just
> to save time and do not reinvent the wheel. I'm looking for the next VMD
> scripts:
>
> # The first one, which would load a trajectory, go through all frames
> centering them by the center of mass (whole system or some particular
> selection) and save the trajectory to a new file.
Tis should do the job:

#load the trajectory
mol new YOUR_TRAJECTORY type TYPE waitfor all
#define the selection you want to be centered
set sel [atomselect top all frame 0}
set num_steps [molinfo top get numframes]
for {set frame 0} {$frame < $num_steps} {incr frame} {
#update the selection to the current frame
        $sel frame $frame
        $sel update
#calculate the center of mass
          set com [measure center $sel ]
#move the com of the sel to origin
        $sel moveby [vecscale -1.0 $com]
}
       $sel delete; unset sel
#write the new trajectory
animate write TYPE NEW-NAME beg 0 end -1 skip 0 0
quit

PLEASE CHECK THE VMD UG FOR ALL THE COMMANDS.

>
> # The second script, which could compute the average residence time of
> hydrogen bonds between the ion and water molecules.
>
> # The third one, which would output the abundance of coordination numbers
> of the ion atoms.
>
>
> It would be great to see some code examples, thanks a lot in advance,
>
> YT, Ivan Degtyarenko
>
> 

-- 
--
eddi
=============================================================================
Eduard Schreiner                     e-mail: eduard.schreiner_at_theochem.rub.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-22121
Ruhr-Universitaet Bochum - NC 03/52         Fax:   ++49 (0)234/32-14045
D-44780 Bochum                              http://www.theochem.rub.de
=============================================================================