VMD-L Mailing List

From: nordgren_at_sas.upenn.edu
Date: Wed Jun 15 2005 - 08:15:10 CDT

OK, I answered my own question... partially...

It turns out that the same functionality alleged to be performed by the
"animate readdel" command can be easily accomplished using the combination
of commands: "animate delete" and "mol addfile".

However, I'm still curious as to why the "animate readdel" command is
broken....

- Erik

C. Erik Nordgren, Ph.D.
Department of Chemistry
University of Pennsylvania

> Hi folks,
>
> OK, it took me a couple days before I could try this out, and sure enough,
> Axel was again correct. Thanks! Yes indeed, a race condition seems to
> have been resulting from my omission of the "waitfor all" option -- even
> though I was only writing a single frame. (I had previously thought that
> this option was only important when reading/writing multiple frames.)
>
> I still have one issue to resolve, however: at the end of the loop in my
> script, I wanted to use the "animate readdel" command, in order to read
> in a new set of coordinates, overwriting the old coordinates. But when
> I tried this:
> animate readdel $out_name.coor beg $frame end $frame
> VMD complains:
> Valid options are: reverse, rev, forward, for, prev, next, pause,
> read, write, delete, and dup.
> So even though the "readdel" option is documented in the user guide, it
> doesn't seem to be recognized by the VMD program! Anybody know what's
> going
> on here? Again, I'm running VMD1.8.3 on IRIX.
>
> Alternatively, is there some other way to do what I want? I tried simply
> using the "animate read" command:
> animate read pdb $out_name.coor beg $frame end $frame waitfor all
> but in this case the new coordinates do not overwrite the old ones; the
> command apparently simply fails (silently!) to do anything, if I try
> reading
> coords into a frame that already has coords. I also tried:
> animate delete beg $frame end $frame
> animate read pdb $out_name.coor beg $frame end $frame waitfor all
> but in this case VMD complains:
> ERROR) molecule_dupframe: frame out of range
> ERROR) Illegal frames requested for coordinate file I/O
>
> Assistance greatly appreciated as always...
>
> - Erik
>
> C. Erik Nordgren, Ph.D.
> Department of Chemistry
> University of Pennsylvania
>
>
> Quoting Axel Kohlmeyer <axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de>:
>
> > On Thu, 9 Jun 2005 nordgren_at_sas.upenn.edu wrote:
> >
> > erik,
> >
> > EN> Unfortunately, I'm still having difficulty of a more subtle nature.
> > Now
> > EN> that I know someone is reading :) I'll elaborate a bit more.
> > Basically,
> >
> > ok. great.
> >
> > EN> what I want to do is use VMD to force a rescaling of the distance
> > between
> > EN> certain parts of my system, and then call NAMD to do some brief
> energy
> > EN> minimization of the coordinates, and then repeat the process in a
> loop
> > EN> over my scaling parameter. At each step, a new coord frame is
> > generated,
> > EN> and at the end the entire trajectory is saved. Here is the skeleton
> > of the
> > EN> VMD script I'm trying to get to work (where the scaling is given by
> > "L")...
> > EN>
> > EN>
> >
> ---------------------------------------------------------------------------
> > EN> mol load psf $start_psf pdb $start_pdb
> > EN> set frame 0
> > EN> # initial coords are left as-is in frame 0; begin minimizing in next
> > frame
> > EN> for {set L [expr $max - $del]} {$L >= $min} {set L [expr $L - $del]}
> {
> > EN>
> > EN> # add new frame to the trajectory, with coords copied from
> current
> > frame
> > EN> animate dup frame $frame 0
> > EN> incr frame
> > EN> animate goto $frame
> > EN>
> > EN> # (modify coords of new frame...)
> > EN>
> > EN> # call NAMD to energy-minimize the new coords
> > EN> animate write pdb $temp_pdb beg $frame end $frame
> >
> > i think here could be the problem. you should add 'waitfor all'
> > to the 'animate write' command, or else VMD will start writing the
> > files and _immediately_ continue executing the script thus creating
> > a race condition. i assume during the first loop this is not
> > biting you, since the parser needs more time to evaluate the
> > script, but from them on it should take advantage of the internal
> > caching of preparse code and thus the writing of the pdb file may
> > not be finished when your script calls NAMD the second time.
> >
> > EN> set cell_size [expr 4.0 * $L]
> > EN> exec env NAMD_psf=$start_psf \
> > EN> NAMD_pdb=$temp_pdb \
> > EN> NAMD_outfile=$out_name \
> > EN> NAMD_minsteps=$namd_minsteps \
> > EN> NAMD_cell=$cell_size \
> > EN> namd2 +p1 $namd_configfile
> > EN>
> > EN> # replace coords of current frame with new (minimized) coords
> > EN> animate read pdb $out_name.coor beg $frame end $frame
> >
> > for safety and the sake of consistency you should add an
> > 'waitfor all' here as well.
> >
> > EN>
> > EN> }
> >
> > best regards,
> > axel.
> >
> >
> > --
> > =======================================================================
> > Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
> > Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673
> > Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045
> > D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
> > =======================================================================
> > If you make something idiot-proof, the universe creates a better idiot.
> >
>
>