Thankyou
On Wed, Apr 10, 2013 at 11:30 PM, Justin Lemkul <jalem...@vt.edu> wrote: > 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 > -- 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
