TCL Combine trajectories

vm_get_index.tcl

############################################################
## TCL script to get index of single chain protein
## Kevin Apr 2014
## Usage  vmd -dispdev text -e <tcl>
## Output  list of index corresponding to atomselect options
############################################################

mol new ../../../ionized.pdb type pdb waitfor all

set sel [atomselect top "protein"]
set file [open index.txt w]

foreach indices [$sel get index] {
  puts $file "$indices"
}

close $file
quit

make_catdcd.sh

#for ii in mini-1 heat pre-npt cons-50 cons-30 cons-10 cons-5 cons-3 cons-1 NPT-1
for ii in {2..3}
do
    filename="$filename ../../output/NPT-$ii.dcd"
done

#catdcd -o prepare.dcd -i index.txt $filename
catdcd -o ups-pro-npt2-3-s50.dcd -i index.txt -stride 50 $filename