From: Maxim Belkin (
Date: Fri Mar 27 2015 - 11:55:05 CDT

Hi Jevgenij,

You have to use catdcd for that purpose. The procedure is the following:

1. Load psf + pdb
2. Make a selection: set sel [atomselect top "selection text"]
3. Write psf of that: $sel writepsf selection.psf
4. Write indices of the selection:
set ch [open indices.txt w]
puts $ch [$sel list]; # [$sel list] is same as [$sel get index]
close $ch
5. Use catdcd to extract your selection from the trajectory:
catdcd -o output_file.dcd -otype dcd -i indices.txt trajectory_file

Good luck,

> On Mar 27, 2015, at 11:43 AM, Jevgenij Raskatov <> wrote:
> Dear users, I am loading a large simulation of a protein in a waterbox into vmd, and would like to only load the protein portion, because otherwise my computer crashes. I understand that one can display the protein only portion, but how about editing it prior to loading, so as to maximize performance?
> Thanks
> --
> Dr. Jevgenij A. Raskatov
> Assistant Professor in Chemistry and Biochemistry
> Tel.: +1-831-459-2978
> Department of Chemistry and Biochemistry
> Physical Science Building 356
> 1156 High Street
> Santa Cruz, CA
> 95064 USA