VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Oct 08 2008 - 10:23:44 CDT

On Wed, 8 Oct 2008, Subramanian Vaitheeswaran wrote:

SV> Dear vmd community,
SV>
SV> I am trying to use the pbctools plugin to unwrap the coords in my test system (a box of waters). I execute this script at the command line:
SV> ****************************
SV> package require pbctools
SV> set outfile [open unwrap.dcd w]
SV>
SV> mol load psf ../solvate.psf dcd h2o.dcd

please don't use this syntax. this is obsolescent.
it is better to use:

set mol [mol new ../solvate.psf type psf waitfor all]
mol addfile h2o.dcd type dcd waitfor all molid $mol

please also note the importance of using "waitfor all"
as normally the script interpreter would advance while
still loading the trajectory.

SV> puts $outfile [pbc unwrap -all]
SV> exit
SV> ****************************

SV> The script terminates without any errors, but the file unwrap.dcd is
SV> empty. What is the correct usage of pbctools? I tried adding the

please read the documentation! the pbc tools change the
coordinates in memory and you have to write it out with
the normal vmd commands to save coordinates (e.g. animate write).

what you are trying to do makes no sense and
is nowhere shown as an example of how to use it.

SV> -verbose option to "pbc unwrap", but this gives an error:
SV> "pbcunwrap: unknown option: -verbose".

cheers,
   axel.

SV>
SV> thanks,
SV> Vaithee
SV> ============================================
SV> S. Vaitheeswaran
SV> Post-doctoral Research Associate
SV> Institute for Physical Science & Technology
SV> Rm 2116, Bldg. 85
SV> University of Maryland
SV> College Park MD 20742
SV> email: vaithee_at_umd.edu
SV> Phone: 301-405-7568
SV> ============================================
SV> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   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.