VMD-L Mailing List

From: nordgren_at_sas.upenn.edu
Date: Fri May 06 2005 - 03:54:18 CDT

Hello all,

I would like to generate a series of coordinate frames using VMD (based upon
manipulations of a single reference configuration) and then analyze the
relative potential energies of the various configurations (using NAMD).

I think the latter part of this will be simple (just do a loop inside NAMD
to read one frame at a time from a DCD file and "run 0" to compute the
energies), but the first part, to my surprise, has proven tricky.

Here is what I tried:
--------
mol load psf $start_psf pdb $start_pdb
set whole [atomselect top all]
set frame 0
for {set z $start_z} {$z >= $final_z} {set z [expr $z - $delta]} {

   (modify my coordinates)

   molinfo top set frame $frame
   # $whole frame $frame
   $whole writedcd $final_dcd
   incr frame
}
--------
This script runs, but the resulting DCD file contains only one frame.

If I un-comment the "$whole frame $frame" line, then the script aborts
on its second trip through the loop; I get an error of:
        atomsel: frame 1 out of range for molecule 0
So I guess my idea of setting the frame number in order to append it
to my DCD output file doesn't work either.

I re-read the VMD manual for the "writeXXX" command (subset of the
"atomselect" command) but there's no detail about how to append frames
one at a time.

I'm sure there's an easier way to do this... can anyone help?

thanks much,
Erik

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