From: Monika Madhavi (
Date: Fri Dec 15 2017 - 05:52:39 CST

Hi all,

I minimized and equilibrated a protein water system. Then I used the final
configuration of this system to start two simulations with the same
parameters except the constraints on backbone atoms. When I calculated the
rmsd using Rmsd visualizer tool, the rmsd starts from two values for the
two trajectories. I used the same reference molecule for both trajectories.
I can't figure out what could be the reason for this. Any insight would be

Thank you

W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.