VMD-L Mailing List

From: Efthymiou, Christos (christos.dereschuk.20_at_ucl.ac.uk)
Date: Fri Jun 17 2022 - 07:26:49 CDT

Hi Norman,

Thank you for the advice. In using the GUI, I have figured out how to export the dcd file with a specific stride value. However, if I try to also remove the water molecules from the dcd file, I then get an error from the program I am using to analyze the simulation as it also requires a psf file. I assume the error arises as the psf file still contains the water molecules, so the total number of molecules in the psf and dcd files do not match. Is there a way to remove the water molecules from the psf file and export it?

Additionally, is catdcd available on Windows? I cannot find any instructions or a manual on how to install and use the program.

Thanks for the help!

Best,
Christos
________________________________
From: Geist, Norman <norman.geist_at_uni-greifswald.de>
Sent: Thursday, June 16, 2022 1:01 PM
To: Efthymiou, Christos <christos.dereschuk.20_at_ucl.ac.uk>; vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: How to reduce the size of a .dcd file?

⚠ Caution: External sender

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!62CcLXJNbxC2gEE416QOjLGZiv_xvkCnvG98QAWx-vHbgJC0p9ad1DZk-v3-pspyfAmseLb1oPNnxcKUImPHSiYr_UZMQ0A$ <https://urldefense.com/v3/__https://eur01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fwww.researchgate.net*2Fpost*2FHow_to_alter_a_large_DCD_file_without_loading_it_on_VMD&data=05*7C01*7Cchristos.dereschuk.20*40ucl.ac.uk*7Ce489352fca184ce8e75508da4f8fed87*7C1faf88fea9984c5b93c9210a11d9a5c2*7C0*7C0*7C637909776825514502*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=6uG3ORuKgmdWF*2Fu7c5QNWcNeQ8U8H5a*2BhAUAmixq4cU*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU!!DZ3fjg!62CcLXJNbxC2gEE416QOjLGZiv_xvkCnvG98QAWx-vHbgJC0p9ad1DZk-v3-pspyfAmseLb1oPNnxcKUImPHSiYraKyn1AM$ > 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.