On Wed, Apr 10, 2013 at 10:43 AM, Preeti Choudhary < preetichoudhary18111...@gmail.com> wrote:
> ---------- Forwarded message ---------- > From: Preeti Choudhary <preetichoudhary18111...@gmail.com> > Date: Wed, Apr 10, 2013 at 7:46 PM > Subject: rmsd > To: gmx-users-ow...@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 -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
