Re: question regarding rmsd

From: Pardis Tabaee (pardis.tabaee.d_at_hotmail.co.uk)
Date: Wed Oct 05 2016 - 10:55:01 CDT

Hi,

What's on the y axis?

Regards,

P

________________________________
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
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: question regarding rmsd

Hi
   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?

thanks
Dhiraj

[Inline image 3]


rmsd.png

This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:22:31 CST