RE: is possible to remove the waterbox before running VMD

From: Wolbach, Jeffrey P \(WOLBACH\) (
Date: Thu Mar 09 2006 - 13:45:20 CST

It is possible, and actually fairly easy, to create a .dcd file
containing only the protein and not the water molecules. Below is a tcl
script to do this.
# Start tcl script
# Initially, load the solvated system psf and dcd files.
mol load psf Swelled_300_Neutral.psf dcd 300_Simulation_2.dcd
# Find the number of frames.
set nf [molinfo top get numframes]
# Loop over each frame, extracting the solute from the solvated system.
# The exact syntax for the atomselect command will vary on a
system-by-system basis.
for {set i 0 } {$i < $nf } {incr i } {
  set sel [atomselect top "protein" frame $i]
  $sel writepdb $i.pdb
# One enters the path to the protein psf file. This psf file should be
for the protein alone,
# not the solvated system!
mol load psf PHK_Trimer.psf
for {set i 0 } {$i < $nf } {incr i } {
  animate read pdb $i.pdb }
# One has to create a unique name for the extracted protein dcd file.
animate write dcd {Tetramer_ReCent_Trio.dcd} waitfor all top
for {set i 0 } {$i < $nf } {incr i } {
    puts "Removing file $i.pdb"
    rm $i.pdb}
# End tcl script
The script is then executed in VMD, in text mode:
    vmd -dispdev text -e scriptname.tcl
After the new .dcd is created you can load and view in VMD like you did
for the solvated system.


From: [] On
Behalf Of lily jin
Sent: Thursday, March 09, 2006 11:34 AM
Subject: namd-l: is possible to remove the waterbox before running VMD

I need the waterbox to do simulation. But when I show the result in VMD,
the waterbox is not necessary, which takes a lot of memory. Is it
possible to do simulation with waterbox and remove it from the
trajectory before displaying in VMD?




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