VMD-L Mailing List

From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Fri Sep 28 2012 - 08:07:27 CDT

Hi Joaquim and Bjornar,

Thanks for your advices.

I tried to incorporate your suggestions but the script still not working properly.

Any other suggestions?

proc gyration { frame } {
   global ref sel all outfile
   $all move [measure fit $ref $sel]
   puts "$frame: [measure rgyr $sel]"
   puts $outfile "[measure rgyr $sel]"
 }
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 1]
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

--- On Fri, 9/28/12, Bjørnar Jensen <bje076_at_ift.uib.no> wrote:

From: Bjørnar Jensen <bje076_at_ift.uib.no>
Subject: Re: vmd-l: Radius of gyration from Big DCD
To: "flavio seixas" <oivalf_nix_at_yahoo.com>
Cc: "VMD List" <vmd-l_at_ks.uiuc.edu>
Date: Friday, September 28, 2012, 11:35 AM

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