From: Pavan Ghatty (pavan.vmd_at_gmail.com)
Date: Sat Nov 11 2006 - 16:11:46 CST

Hello all,

Following are the contents of the file that I used in the command "vmd
-dispdev text -e FILE.dat". FILE.dat is supposed to give me the rmsd data
for 50 steps [which is the no. of frames]. I tried doing this in the normal
fashion by opening vmd's GUI first and the typing the commands in console.
That worked fine[Got data for all 50 steps]. While doing that I saved the
commands to FILE.dat and to my surprise, all commands except "set,for and
close" got logged. I then went ahead and wrote the commands to
FILE.datmyself and tried using "vmd -dispdev text -e
FILE.dat". This stopped at the 6th step. On punching "vmd -e FILE.dat", I
saw that Tkconsole was activated before all the 50 frames were loaded which
would mean that the rmsd calculations began before all the frames got loaded
(apparently only 6 got loaded) and hence, stopped giving out data after the
6th step. Is there a way to get around the problem ?

# VMD for LINUX, version 1.8.4 (April 17, 2006)
# Log file 'Obtaindatavmd.dat', created by user pkc
menu files off
menu files on
animate style Loop
display resetview
mol new {/tmp/bio-pre/WT10/10wt.top} type {parm7} first 0 last -1 step 1
waitfor 1
animate style Loop
mol off 0
display resetview
mol addfile {/tmp/bio-pre/WT10/reimaged_and_centered_to_all.mdcrd} type
{crdbox} first 0 last -1 step 1 waitfor 1 0
animate style Loop
mol on 0
menu tkcon off
set sel [atomselect top "resid 33 to 61"]
set chan [open reimaged_and_centered_to_all.mdcrd_RMSD w]
for {set i 0} {$i < [molinfo top get numframes]} {incr i} {puts $chan [list
$i [frame_rmsd $sel $i 0]]}
close $chan
menu tkcon on
# VMD for LINUX, version 1.8.4 (April 17, 2006)
# end of log file.

PS: I also tried "for {set i 0} {$i < 50} {incr i} {puts $chan [list $i
[frame_rmsd $sel $i 0]]}" and ended up with "frame_rmsd: frame number out of
range" which clearly implies that VMD does not wait for all the frames to
load.
"proc frame_rmsd" was sourced to .vmdrc file.