VMD-L Mailing List

From: Jacob Layton (jrlayto1_at_asu.edu)
Date: Wed Mar 06 2024 - 13:43:16 CST

Hello,

The basic idea is to count the number of water molecules inside the water
channel of my protein for each frame of a trajectory. The issue is that the
protein is not fixed in space, and simply defining the area using
selections such as "x > -10 and x < 10 and y > 20 and y < -20 and z > 25
and z < -25" (used in one of my previous counts) doesn't account for the
protein's movement and will eventually include waters not present in the
channel.

I'm not sure if it would be possible using tcl scripting to assign certain
residues as "boundaries" for the water channel region. Or perhaps adding a
dummy atom at the center of mass of the region that would move alongside
the trajectory. I did notice the gromacs water transition count tool from a
previous thread here (
https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/25483.html) and
have been contemplating whether it would be worthwhile to convert my namd
files. Any insight would be appreciated.