From: Raman Preet Singh (
Date: Thu Aug 12 2021 - 12:44:46 CDT

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.