VMD-L Mailing List

From: Subramanian Vaitheeswaran (vaithee_at_umd.edu)
Date: Wed Oct 08 2008 - 08:21:10 CDT

Dear vmd community,

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:
****************************
package require pbctools
set outfile [open unwrap.dcd w]
                                                                                
mol load psf ../solvate.psf dcd h2o.dcd
puts $outfile [pbc unwrap -all]
exit
****************************
The script terminates without any errors, but the file unwrap.dcd is empty. What is the correct usage of pbctools? I tried adding the -verbose option to "pbc unwrap", but this gives an error: "pbcunwrap: unknown option: -verbose".

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