removing water from big dcd files

From: jose correa (
Date: Tue Mar 03 2009 - 20:36:24 CST

Dear NAMD users
I have a big *dcd file (10 GB), then, i can not open it in vmd, looking
about the same problems, i applied the next scrip that was suggested in this
forum, however, after run it in vmd Tk console show: can not read "nf" no
such variable, unable to load structure file dry_prot.psf, can not reat nf"
no such variable, invalid command. Any suggestion?, please.
 mol load psf solvated.psf
  for {set i 0 } {$i < $nf } {incr i 100 } {
     animate read dcd md0001.dcd beg i end i
     set sel [atomselect top protein]
     $sel writepdb $i.pdb
     if { $i == 0 } {
        $sel writepsf dry_prot.psf
     $sel delete
     animate delete all
  mol delete top
  mol load psf dry_prot.psf
  for {set i 0 } {$i < $nf } {incr i 100 } {
      animate read pdb $i.pdb
      file delete $i.pdb
  animate write dcd {myprotein_prot.dcd} waitfor all

 best wishes

j correa-basurto

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