VMD-L Mailing List

From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Thu Sep 27 2012 - 14:08:31 CDT

Hi,

I based in the Tcl tutorial on www.tcl.tk as well vmd-list to make the script below aiming to calculate the gyration radius over simulation time from a BigDCD file.

proc gyration { frame } {
   global ref sel all outfile
   $all move [measure fit $sel $ref]
   puts "$frame: [measure rgyr $sel $ref]"
   puts $outfile "[measure rgyr $sel $ref]"
 }
set mol [mol addfile CALDHmT178_wb_min4.coor type pdb waitfor all]
set all [atomselect $mol all]
set ref [atomselect $mol "protein and backbone and noh" frame 0]
set sel [atomselect $mol "protein and backbone and noh"]
set outfile [open gyration.dat w]
bigdcd measure dcd CALDHmT178_wb_eq5.dcd
bigdcd_wait
close $outfile

However, after running there is nothing on output file gyration.dat

I am not a developer, just an user and I am not able to find the error.

Does someone could give me a clue about what is missing in the script above?

Thanks for any help.

Flavio