VMD-L Mailing List

From: Fred (Rui FENG) (fengruifree_at_gmail.com)
Date: Thu Feb 26 2009 - 15:00:53 CST

Hi All,

The manual says when tcl command "animate delete all" is executed, VMD
will delete all the frames from the memory. But when I check the
memory from the Windows Task Manager, the memory doesn't reduce much.
Because I'm trying to read a 2.4 GB dcd file frame by frame to
calculate RMSD, VMD will use up the memory. The Tcl code is below:

# codes start
set dcdfile C:/test.dcd
set outfile [open rmsd.dat w]

# rmsd calculation loop
for { set i 100 } { $i <= 200 } { incr i } {
        animate delete all
        mol addfile $dcdfile type dcd first 0 last 0 step 1 filebonds off
autobonds off waitfor all
        set frame0 [atomselect top "name N" frame 0]

        mol addfile $dcdfile type dcd first $i last $i step 1 filebonds off
autobonds off waitfor all
        set sel [atomselect top "name N"]
        $sel frame $i
        $sel move [measure fit $sel $frame0]
        puts $outfile "$i [measure rmsd $sel $frame0]"
        puts $i
}
close $outfile
animate delete all
# codes end

Do you know how to slove the out-of-memory problem? Thank you!

Have a nice day!

Fred