---------- 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 ? -thankyou -- 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
