VMD-L Mailing List

From: ROPÓN-PALACIOS G. (groponp_at_gmail.com)
Date: Tue Mar 21 2023 - 16:25:47 CDT

Dear All,

I am trying to calculate the osmotic permeability (mp) of an aquaporin tetramer, for each monomer. In relation to this I have 2 questions,

1. When I make the selection :
" (rename TIP3 and name OH2) and z>=-9 and z<=9 and (x^2+y^2)<7^2”
, if I don't apply update selection, I see the water molecules scattered everywhere, but this doesn't It happens if I make "rename TIP3", it is seen in this last selection how the water enters the 4 monomers, but if I make the previous selection, if I do not apply update it does not give me a visualization of the water molecules entering the channel, if not everything, anywhere. My question is what is the correct selection that I would have to make if I want to calculate the MSD of my molecules for each monomer only along the Z axis?

Thank you very much if someone can help me with this, because it is a bit confusing