VMD-L Mailing List

From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Fri Dec 15 2017 - 04:55:54 CST

Hi all,

I minimised 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 visualiser tool, the rmsd starts from two values for the
two trajectories. I can't figure out what could be the reason for this. Any
insight would be appreciated.

Thank you
Best,
Monika