From: Leandro Martínez (leandromartinez98_at_gmail.com)
Date: Wed Oct 05 2016 - 15:58:39 CDT
Concerning references for RMSD calculations, you might want to take a look
at this package we developed:
It computes the RMSD while identifying the most conserved regions within
the structure, and uses those regions as a reference for the alignment.
It can help to interpret what is actually going on in your simulations if
average fluctuations seem to be large.
On Wed, Oct 5, 2016 at 5:39 PM, Radak, Brian K <bradak_at_anl.gov> wrote:
> In my opinion, if you want to quantify the fluctuations, you have to be
> careful in what you choose as your reference for RMSD - looking for
> anomalous domains, as you have, is probably an excellent idea (and much
> more informative than simply saying "the RMSD is noisy").
> Long equilibration times are absolutely acceptable, especially if you are
> not so sure the initial conditions are physically realistic or relevant.
> Coming from the nucleic acids community we regularly expect equilibration
> times > 50 ns - I try to take people at their word when they say a protein
> system equilibrated faster than that, but it always seems overly fortuitous
> to me.
> There are a number of analyses that might be useful for comparing with B
> factors - principle component analyses is probably the most popular. A
> cluster analyses is also probably a good idea (and might provide a better
> reference for RMSD calculations).
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
> 9700 South Cass Avenue, Bldg. 240
> Argonne, IL 60439-4854
> (630) 252-8643
> *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:* Wednesday, October 05, 2016 2:02 PM
> *To:* namd-l_at_ks.uiuc.edu; Pardis Tabaee
> *Subject:* Re: namd-l: question regarding rmsd
> Thank you Everyone.
> The simulation was started from crystal structure obtained by
> cocrystallizing with ligand. I don't see any significant difference in apo
> vs ligand bound form but ligand is an inhibitor. I think for unstable
> RMSD, I can blame a small flexible domain. After removing the flexible
> domain from RMSD calculation, I got stable RMSD very similar to apo
> protein. However its still took long time to equilibrate. the sudden change
> in rmsd at around 30 ns is still there. can I use data after 40 ns for the
> analysis? is it acceptable to have such a long equilibration time? I am
> primarily a crystallographer and I don't have much experience in publishing
> articles with MD simulation data. So I don't know what's acceptable in the
> community? I am doing simulation to find out if allosteric behaviour of
> ligand is due to change in dynamics. I would like to compare it with B
> factor change in crystal structure.
> On Wed, Oct 5, 2016 at 1:34 PM, Pardis Tabaee <
> pardis.tabaee.d_at_hotmail.co.uk> wrote:
>> 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:* owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of
>> Radak, Brian K <bradak_at_anl.gov>
>> *Sent:* 05 October 2016 17:18
>> *To:* namd-l_at_ks.uiuc.edu; Roshan Shrestha; dhirajks_at_gmail.com
>> *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:* 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> 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> wrote:
>>> 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
>>> *To:* namd-l_at_ks.uiuc.edu
>>> *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?
>>> [image: Inline image 3]
>> Roshan Shrestha
>> Graduate Student
>> Central Department of Physics,Tribhuvan University
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