[gmx-users] Fwd: rmsd
preetichoudhary18111989 at gmail.com
Thu Apr 11 15:47:41 CEST 2013
On Wed, Apr 10, 2013 at 11:30 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
> > I used as an input in for my final mdrun.I am getting rmsd of about 5
> > 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,
> > 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
> > 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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