[gmx-users] Fwd: rmsd

[Preeti Choudhary]

---------- Forwarded message ----------
From: Preeti Choudhary <preetichoudhary18111989 at gmail.com>
Date: Wed, Apr 10, 2013 at 7:46 PM
Subject: rmsd
To: gmx-users-owner at gromacs.org


Hi,
I calculated the rmsd of my md simulation trajectory by giving the tpr file
I used as an input in for my final mdrun.I am getting rmsd of about 5 A.now
when I calculated the rmsd of my md simulation trajectory by giving the
last frame of my equlibrated trajectory/first frame of my md trajectory, I
see highly fluctuating rmsd ,with an average rmsd of about 15 A. Now the
first frame of my md trajectory is similar to the .tpr file- input I give
for my mdrun ,then why such huge variation is coming???Please explain this
difference?ideally I should calculate the rmsd using which file-.tpr file
or .gro file of equlibration ?

-thankyou