From: Axel Kohlmeyer (
Date: Fri Jul 18 2008 - 12:08:25 CDT

On Thu, 17 Jul 2008, Maria Sanchez Farran wrote:

MSF> Hi everyone,

dear maria antonieta,


MSF> As it was suggested in previous postings, I tried this approach
MSF> (after loading the psf and dcd files)

MSF> source the following script:
MSF> set nframes [molinfo top get numframes]
MSF> for {set i 0} {$i < $nframes} {incr i} {
MSF> molinfo top set frame $i
MSF> molinfo top set a xx
MSF> molinfo top set b yy
MSF> molinfo top set c zz
MSF> }

for this to work you have to replace xx, yy, zz with the values
of x, y, z-length of your box. right now you are using an illegal
value that will be interpreted as 0.0.

MSF> source unwrap.tcl
MSF> unwrap -all

MSF> When I run all the commands it read " box abnormally small or no
MSF> box size available" I think that the problem I am facing is that I

exactly. you didn't set the box.

BTW: did you do a constant volume calculation?
the loop to set the box only works on for fixed volume.

MSF> didn't specified "DCDUnitCell yes" in the .conf file. From the NAMD
MSF> manual, it seems that 'yes" is the default value if we are using
MSF> PBC, but it seems that they are not there. I tried getting them
MSF> from the xst file using pbc tools with

MSF> package requires pbctools
MSF> pbc readxst -all

MSF> and then run both scripts. But it didn'work. I also tried to use

of course not. please read the pbctools documentation.
you didn't specify the .xst file name. how should it work?

MSF> pbc unwrap -all instead of using the unwrap.tcl, but it didn't work
MSF> either. My question is, what do I need to do after reading the xst
MSF> file. Do I need to write a new trajectory file after reading the
MSF> real coordinates from the xst file, load this new dcd file, and
MSF> then run the other two scripts?

the key to your troubles is that you need to have the box information
set correctly for all cases and then the pbctools' option should work
ok. you may want to download the latest alpha test version of VMD.
several bugfixes and improvements have been added to the pbctools
package and the documentation matches the lastest development version
of VMD and not the current release...


MSF> Thank you for your help!
MSF> Maria Antonieta

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.