From: Raman Preet Singh (
Date: Fri Aug 13 2021 - 08:41:18 CDT

Dear Josh,

Thank you very much for your reply and directions. Really helpful!


From: Vermaas, Josh <>
Sent: Friday, August 13, 2021 1:25:03 AM
To: Raman Preet Singh <>; <>
Subject: Re: vmd-l: Stripping water from psf

Hi Raman,

Whatever atomselection you use for exporting can also be used for writing a psf. For instance:

set nowat [atomselect top “not water”]

$nowat writepsf nowat.psf

animate write dcd nowat.dcd waitfor -1 sel $nowat

Will take a loaded trajectory (specifically the top one), and write a new psf and dcd file with only the atoms that match the selection.


From: <> on behalf of Raman Preet Singh <>
Date: Thursday, August 12, 2021 at 2:32 PM
To: "" <>
Subject: vmd-l: Stripping water from psf

Dear VMD users,

I have a big NAMD trajectory file (dcd file) which I would like to analyze using VMD. I loaded the PSF and DCD in VMD, used representation "not water" to hide all water molecules and saved the trajectory as dcd. This gave a DCD with water stripped off. However, I am not sure how to remove water from psf.

I looked into the mailing list and NAMD/VMD tutorials where others have exported only the protein to obtain a PSF with all non-protein components stripped. However, those commands could not be directly applied since many of my systems contain a small molecules or a polysaccharide or a nanoparticle. These components may be present either alone in or in different combinations (protein-sugar, protein-small molecule, protein-nanoparticle, sugar-nanoparticle, etc.....). Other components include water and ions.

I will be thankful for any direction on stripping water from psf.