VMD-L Mailing List

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

Hi,
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.
https://www.ks.uiuc.edu/Development/MDTools/catdcd/

-Josh

From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of "Efthymiou, Christos" <christos.dereschuk.20_at_ucl.ac.uk>
Date: Thursday, June 16, 2022 at 7:24 AM
To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: How to reduce the size of a .dcd file?

Hello,

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.