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From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Fri Sep 28 2012 - 09:58:31 CDT
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Hi Bjornar,
Many thanks for your help. Its working fine now.
I will post the script here for future references.
Best regards,
Flavio
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 protein.pdb 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 gyration dcd protein.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, 2:39 PM
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
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