CatDCD

Single dcd

First: Make an index file

set filename "1chain_A_wt"

#mol new ionized.pdb type pdb waitfor all
# set sel [atomselect top "((resid >=1 and resid <=28) or (resid >=134 and resid <=140)) and name P"]
set sel [atomselect top "chain A"]
# set indices [$sel get index]

set file [open $filename.ind w]
foreach indices [$sel get index] {
 puts $file "$indices"
}

# flush $file
close $file

Save it as a tcl script.

Load your molecule manually or uncomment the molecule loading command in the script (with your molecule name replaced).

Then

source getind.tcl

in the Tk Console. You will get your index file with the file name you have defined in the first line.

Second: catdcd

Get your dcd and ind file in the same directory. Simply

catdcd -o output.dcd -i index.ind trajectory.dcd

does the job.

Multiple dcd

First: Make an index file

foreach i {A B C D E F G H I J K L M N O P Q R S T U V W X} {

set filename "1chain+$i+wt"
set sel [atomselect top "chain $i"]
set file [open $filename.ind w]

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

Second: catdcd

#!/bin/bash
for i in A B C D E F G H I J K L M N O P Q R S T U V W X
do
 catdcd -o 1chain+$i+wt.dcd -i 1chain+$i+wt.ind NPT-4.dcd
done

Get xyz instead of dcd

#!/bin/bash
for i in {1..24}
do
  catdcd -o 1chain+P$i+wt+CA+dcd.xyz -otype xyz -i 1chain+P$i+wt+CA.ind -stype pdb -s MjHSP16.5_wt_CA.pdb -first 4050 -last 4500 NPT-4_CA.dcd
  catdcd -o 1chain+P$i+wt+CA+ref.xyz -otype xyz -i 1chain+P$i+wt+CA.ind -stype pdb -s MjHSP16.5_wt_CA.pdb -first 4050 -last 4050 NPT-4_CA.dcd
done

Convert binary DCD to xyz

catdcd -o output.xyz -otype xyz -s struct.psf -stype psf somedcd.dcd

or

catdcd -o output.xyz -otype xyz -s struct.pdb -stype pdb somedcd.dcd