VMD-L Mailing List

From: Jason Smith (jason_smith_18_at_sfu.ca)
Date: Thu Jan 21 2021 - 10:54:12 CST

Hi Surya,

I'm not sure what you mean by 'keep'. You can select them using e.g. in the representation window:

water and (same residue as within X of protein)

where X is a distance in angstroms (this won't capture ions btw). But you're gonna have to be more specific about what you want to do after that. Bear in mind that you will need to update the selection every frame to keep only the solvent in close proximity to the protein.

Cheers,

-
Jason Smith
Post-Doctoral Fellow
Robert N. Young Lab, Simon Fraser University
8888 University Drive, Burnaby, BC, V5A-1S6
Canada

________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Seera Suryanarayana <palusoori_at_gmail.com>
Sent: Wednesday, 20 January 2021 9:15:37 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: How to keep particular water molecules within the cut off during the simulations

Dear VMD users,
I have done simulations of 15 residue length protein in water with the help of gromacs. Now I have to keep the water molecules which are close to the amino acids. Please tell me how to do it in vmd.

Thanks in advance
Surya
Graduate student
India.