VMD-L Mailing List

From: Geist, Norman (norman.geist_at_uni-greifswald.de)
Date: Thu Jun 16 2022 - 07:01:13 CDT

Hi,

you can use a "stride" value when using the GUI to load your files.
Away from that, catdcd is the best tool for such operations. I also
suggest removing for example the water from the DCD files to reduce
the size, in case you will not need it for your analysis. Look
here https://urldefense.com/v3/__https://www.researchgate.net/post/How_to_alter_a_large_DCD_file_without_loading_it_on_VMD__;!!DZ3fjg!8JhVboqkmd6_fl9qwOWMuQ0r2LKeLZvWqyf2rYRCCXIki3ImnKueoz7JIBkAw07iwSEyv0jgtimPhGn9quXYhY3DnFXcUklMEg$  for
exmaples.

Bests
Norman Geist
Am Donnerstag, den 16-06-2022 um 12:14 schrieb Efthymiou, Christos:

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.