Re: question regarding rmsd

From: Pardis Tabaee (
Date: Wed Oct 05 2016 - 13:34:41 CDT

I think it's the average RMSD that was calculated. Maybe you can try to equilibrate without the solvent and see if you reach a stable conformation of your complex quicker than if you do it with the solvent? There are also other strategies. SMD is one of them, where you are applying constraints, you can do this with NAMD.

From: <> on behalf of Radak, Brian K <>
Sent: 05 October 2016 17:18
To:; Roshan Shrestha;
Subject: RE: namd-l: question regarding rmsd

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.


Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory

9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
From: [] on behalf of Roshan Shrestha []
Sent: Wednesday, October 05, 2016 11:07 AM
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, <<>> 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 <<>> wrote:


What's on the y axis?



From:<> <<>> on behalf of Dhiraj Srivastava <<>>
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?


[Inline image 3]

Roshan Shrestha
Graduate Student
Central Department of Physics,Tribhuvan University


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