From: Radak, Brian K (bradak_at_anl.gov)
Date: Wed Oct 05 2016 - 11:18:12 CDT
I'm not clear what the "problem" is here. Are you not happy with the (large?) oscillations after 100 ns? I don't understand why you would be surprised that convergence to a stable state takes that long. I'm more surprised that the apo state levels out in 20 ns.
I presume this is RMSD with respect to the initial frame, as is default for VMD? That's a completely arbitrary reference and thus I wouldn't hold too much stock in it. Is the initial bound state from a crystal structure or was it generated by docking to the apo structure? If the latter, then there isn't really a reason to believe the initial configuration had a high Boltzmann weight anyway - slow equilibration is to be expected and could involve large conformational changes.
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From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of Roshan Shrestha [roshanpra_at_gmail.com]
Sent: Wednesday, October 05, 2016 11:07 AM
To: namd-l_at_ks.uiuc.edu; dhirajks_at_gmail.com
Subject: Re: namd-l: question regarding rmsd
Don't worry dhiraj, it's obviously rmsd in Y-axis and Time steps in X-axis. Shouldn't have been any fuss with it !!!
On Wed, Oct 5, 2016 at 9:48 PM, <dhirajks_at_gmail.com<mailto:dhirajks_at_gmail.com>> wrote:
Sorry. I should have labeled it. Y axis is time in picosecond and x axis is rmsd in Angstrom.
Sent from my iPhone
On Oct 5, 2016, at 10:55 AM, Pardis Tabaee <pardis.tabaee.d_at_hotmail.co.uk<mailto:pardis.tabaee.d_at_hotmail.co.uk>> wrote:
What's on the y axis?
From: owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu> <owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>> on behalf of Dhiraj Srivastava <dhirajks_at_gmail.com<mailto: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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-- Roshan Shrestha Graduate Student Central Department of Physics,Tribhuvan University Kathmandu,Nepal
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