VMD-L Mailing List

From: Raman Preet Singh (ramanpreetsingh_at_hotmail.com)
Date: Thu Jun 16 2022 - 08:23:34 CDT

Strip water, that will reduce the size considerably (tens to a few hundred MB, depending on how much water is there).

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From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Efthymiou, Christos <christos.dereschuk.20_at_ucl.ac.uk>
Sent: Thursday, June 16, 2022 3:44:03 PM
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.