VMD-L Mailing List

From: Natal Kanaan (kanaan_at_zedat.fu-berlin.de)
Date: Tue Aug 12 2014 - 06:30:30 CDT

Dear all,
I'm trying to write a pdb structure which is an average of several
trajectories. Searching in the list, I found a script similar to the one
below, but I don't know how to really write this new-averaged-pdb
structure:

set mol [mol new ../model8_final/setup/model8_ionized.psf type psf waitfor
all]
mol addfile model8_R3_parte1.dcd type dcd waitfor all
mol addfile model8_R3_parte2.dcd type dcd waitfor all
mol addfile model8_R3_parte3.dcd type dcd waitfor all
mol addfile model8_R3_parte4.dcd type dcd waitfor all
set sel [atomselect $mol all]
measure avpos $sel

Any kind of help would be really appreciated. Another issue is that, as I
have a lot of data, if I just source this script directly in vmd, it ends
up being "killed". I already tried with:

vmd -dispdev text -e xx.tcl

but it is also killed.
Thanks a lot in advance for your help,
Natal