From: Vermaas, Josh (
Date: Thu Jun 16 2022 - 07:57:50 CDT

There are about a bajillion ways to do this.
In VMD, you can do something like:

mol new system.psf
mol addfile dcdfile.dcd step 50 waitfor all
animate write dcd newdcdfile.dcd

There is also the catdcd program that can do manipulations without firing up VMD.


From: <> on behalf of "Efthymiou, Christos" <>
Date: Thursday, June 16, 2022 at 7:24 AM
To: "" <>
Subject: vmd-l: How to reduce the size of a .dcd file?


I have run several molecular dynamics simulations on a protein-protein complex that I would like to analyze with different python programs I have found online. However, the file size of my production run is around 5 GB and seems to overwhelm the programs and the memory I have on my computer. Is there a way to reduce the size of a .dcd file? For example, create a new .dcd file that only has every 50th frame of the original? I have a Windows 10 computer with the 32bit and 64bit versions of VMD available.

Thanks in advance.