[gmx-users] Fwd: rmsd

Justin Lemkul jalemkul at vt.edu
Wed Apr 10 20:00:18 CEST 2013

On Wed, Apr 10, 2013 at 10:43 AM, Preeti Choudhary <
preetichoudhary18111989 at gmail.com> wrote:

> ---------- 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 ?
The choice of reference structure depends on what you are trying to study.
The fact that the "forward" and "reverse" RMSD values are different is not
necessarily surprising. Using a .tpr file allows you to deal well with PBC
effects; using a coordinate file does not, unless you have done adequate
re-imaging and/or fitting.




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)


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