VMD-L Mailing List

From: Θωμας Ευαγγελιδης (te8624_at_mbg.duth.gr)
Date: Tue Sep 11 2007 - 17:26:12 CDT

Dear Leo,
I did what you advised me and then tested bigdcd in various cases. It worked
perfectly in all of them.
Thanks a lot!
Thomas

> Hi Thomas,
>
> Try changing the following line in bigdcd_done:
>
> after idle uplevel #0 trace vdelete vmd_frame w bigdcd_callback
>
> to
>
> uplevel #0 trace vdelete vmd_frame w bigdcd_callback
>
> Please let me know if it solves your problem.
>
> Best,
> Leo
>
> On Tue, Sep 11, 2007 at 09:56:32PM +0300, Θωμας Ευαγγελιδης wrote:
> > 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
> > >
> >
> >
> >
>
> --
> Leonardo Trabuco, Ph.D. student
> Theoretical and Computational Biophysics Group
> University of Illinois at Urbana-Champaign
>