From: Maria Sanchez Farran (
Date: Thu Jul 17 2008 - 21:40:46 CDT

Hi everyone,
I would like to receive some advice regarding the transformation of pbc coordinates to real coordinates from a trajectory with "wrapAll on". I am interested in calculating the mean square displacement of the water molecules that are in the hydration layer, so I need to determine the distance that those water molecules have moved, compare it to the previous frame, and average the total distance over the number of molecules (right now I am looking at the same molecules in all frames, but I I will then update the list of molecules in each frame).
As it was suggested in previous postings, I tried this approach (after loading the psf and dcd files)
source the following script:
set nframes [molinfo top get numframes]
for {set i 0} {$i < $nframes} {incr i} {
  molinfo top set frame $i
  molinfo top set a xx
  molinfo top set b yy
  molinfo top set c zz
source unwrap.tcl
unwrap -all
When I run all the commands it read " box abnormally small or no box size available" I think that the problem I am facing is that I didn't specified "DCDUnitCell yes" in the .conf file. From the NAMD manual, it seems that 'yes" is the default value if we are using PBC, but it seems that they are not there. I tried getting them from the xst file using pbc tools with
package requires pbctools
pbc readxst -all
and then run both scripts. But it didn'work. I also tried to use pbc unwrap -all instead of using the unwrap.tcl, but it didn't work either. My question is, what do I need to do after reading the xst file. Do I need to write a new trajectory file after reading the real coordinates from the xst file, load this new dcd file, and then run the other two scripts?
Thank you for your help!
Maria Antonieta