VMD-L Mailing List

From: K Jan (10dunajkr_at_gmail.com)
Date: Thu Jan 07 2021 - 18:18:59 CST

`m trying to calculate the RMSD of a 90 ps simulation of a molecule with
cpptraj.

The rmsd increases from 0 to 17 Angstroms in the 90 ps which is clearly too
big. I`ve also checked the vmd and my molecule is translating around the
screen a small amount and vibrating a little, but the structure of it
doesn't change at all, which is strange because the radius of gyration has
increased, which should mean that the compactness of my molecule has
decreased but that hasn`t happened.

I read that I have to perform a least-squares fit to remove the global
rotation and translation. I am not sure how to do this and would appreciate
some advice. I read that I could do this on the vmd by using the rmsd
trajectory tool but when I try and press align in the tool it says that no
atoms have been selected, even though I wrote protein in the atom selection
box, and I have loaded up the topology of my molecule and the trajectory
files from my simulation.

Would appreciate some help.

Thanks ,
Kris