VMD-L Mailing List

From: Θωμας Ευαγγελιδης (te8624_at_mbg.duth.gr)
Date: Tue Sep 11 2007 - 13:56:32 CDT

Leo,
this is not an option, my script is too big!
Try to run the following simple script instead, just to see what I mean:

play mybigdcd.tcl

mol load psf DCD_with_cell.psf

proc write { frm } {
if {$frm>51} {
return
}
puts "frame=$frm"
animate write pdb wholeframe_$frm.pdb beg 0 end 0 waitfor all top
}

bigdcd write DCD_with_cell.dcd

bigdcd_wait_till_done

for {set i 1 } {$i<=51} {set i [expr $i+10]} {
puts "i=$i,"
mol load pdb wholeframe_$i.pdb
}

My trajectory is DCD_with_cell and it has 51 frames. Can you see that return
inside proc write? If I include it everything works fine, but if I omit it, VMD
does its job correctly but at the end it tries to write more frames than 51 (it
goes up to 55) and at the output I get "Illegal frames requested...".
One way you could help me is by finding a way to get the number of frames of a
trajectory while using bigdcd to load it.I have tried to set a global variable
$num_frames inside bigdcd proc in various ways, but nothing worked.

Thomas

> Hi,
>
> If you send me the script I can take a look at it...
>
> Cheers,
> Leo
>
> On Tue, Sep 11, 2007 at 06:07:23PM +0300, Θωμας Ευαγγελιδης wrote:
> > Leo,
> > yes I tried that too, it worked good up to the 6th frame (if I remember
> > correctly) and then failed again. Whenever I didn't do that it failed
> > instantly.
> > Thomas
> >
> > > On Tue, Sep 11, 2007 at 02:19:53PM +0300, Θωμας Ευαγγελιδης wrote:
> > > > I used "mybigdcd.tcl" in my code and everything worked fine. Now I
> > > > confront another difficulty. The code that I described in my previous
> > > > message was a part of a bigger program. That program uses bigdcd twice
> > > > and while the first proc is executed correctly, the second proc fails
> > > > to terminate.
> > >
> > > Did you try sourcing mybigdcd.tcl again before running the second proc?
> > > From a quick look, that seems necessary at least to set the variable
> > > $bigdcd_is_done back to zero.
> > >
> > > Cheers,
> > > Leo
> > >
> > > --
> > > Leonardo Trabuco, Ph.D. student
> > > Theoretical and Computational Biophysics Group
> > > University of Illinois at Urbana-Champaign
> > >
> >
> >
> >
>
> --
> Leonardo Trabuco, Ph.D. student
> Theoretical and Computational Biophysics Group
> University of Illinois at Urbana-Champaign
>