From: Bjørnar Jensen (bje076_at_ift.uib.no)
Date: Fri Sep 28 2012 - 05:35:53 CDT

Hello,

while it may or may not solve your problem, there seems to be an error
in your script
related to the [measure rgyr] command.

According to the user manual:
http://www.ks.uiuc.edu/Research/vmd/current/ug/node136.html
*rgyr /selection/ [weight /weights/]*: Returns the radius of gyration of
atoms in /selection/ using the given weight.

Note how this command only accept ONE selection, while your use of the
command is:

[measure rgyr $sel $ref]

,where you're using two selections.

When using the measure command in your manner in the TkConsole, I get:

55 % measure rgyr $sel $sel2
wrong # args: should be "measure rgyr <selection> [weight <weights>]"

Basically, you're not getting any data in your file as the script aborts
whenever it reaches this command.

Best regards,
Bjørnar

On 2012-09-27 21:08, flavio seixas wrote:
> 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
>
>
>
>