From: Pardis Tabaee (pardis.tabaee.d_at_hotmail.co.uk)
Date: Wed Oct 05 2016 - 10:55:01 CDT
What's on the y axis?
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Dhiraj Srivastava <dhirajks_at_gmail.com>
Sent: 04 October 2016 22:07
Subject: namd-l: question regarding rmsd
I am trying to do MD simulation on a protein with and without ligand. when I did rmsd plot, I found that apo protein is behaving fine (red) but ligand bound form (black) is taking relatively longer time to equilibrate and showing quite a bit of fluctuation in rmsd. is the fluctuation in rmsd value for ligand bound protein is acceptable or is there anything wrong? How can I fix it?
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