the RMSD calculations remove rigid-body tumbling by default, unless you use
something like the "nofit" flag in cpptraj. Otherwise it will include
internal motions only, and be sensitive to the reference structure. In my
opinion, when the RMSD values are high (such as 5-6), the RMSD
fluctuations are not meaningful to interpret since the reference structure
is no longer similar. Resetting the reference may improve the significance
of the RMSD fluctuations.
The energy discontinuity after 10,000 on the X axis looks to me to be a
typical artifact of the plotting program and likely does not exist in the
actual data set. This often happens in programs such as xmgrace when the
number of data points loaded exceeds compiled limits. Try a different
plotting program, or use a program like vi to look at the energy values in
that region- they likely are simply not being plotted by the program. Your
actual energy fluctuations will depend on the thermostat and may not
reflect significant events in the conformational dynamics of the solute.
On Sun, Feb 21, 2021 at 11:13 AM Gordon Richard Chalmers <gordoncs.uga.edu>
wrote:
>
> Checking protein-ligand contact distances in the simulation is probably
> the best move. Couple more quick points with my 2 cents:
>
> Energy fluctuations like the discrete one found in your plot
> can be explained by the presence of distance thresholds of an interaction
> in the force field forcing the interaction to turn off or on. If the
> ligand
> is in fact in the process of disassociating from the protein or rotating
> very slowly then this could explain the discrete jump.
>
> The RMSD fluctuations are expected from internal motion and also from
> real-world non-isotropic rigid body tumbling and compared to the initial
> state.
>
> I would expect an equilibration or simulation time of 25 to 50 the
> tumbling time of your system (or just the ligand) to accurately use the
> trajectory in a physical calculation.
> At that order. 100 ns would be appropriate for a molecule of about 8 to
> 4 kDa, or more depending on what the purpose of the simulation and
> what observable you are estimating from MD, not taking into account
> any conformational changes.
>
> The simulation has not plateaued halfway it appears. It is still linearly
> increasing linearly from ~4 about to ~5 in 60, slower than ~1 to ~4 in
> the 1st 60.
>
> Gordon Chalmers
>
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Sunday, February 21, 2021 8:58 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Sufficiently equilibrated or not
>
> [EXTERNAL SENDER - PROCEED CAUTIOUSLY]
>
>
> I think it's important to visually examine your trajectories, not just
> calculate rmsd. is that the rmsd of the ligand fit to itself? if so it can
> stay low even if the ligand dissociates. It might be better to calculate
> distances for the key ligand-DNA contacts and make sure they are staying
> close.
>
> for your DNA rmsd, 5A seems quite high, but it really depends strongly on
> the system you have. Is the DNA long? Normal bending motions can give large
> RMSD, as can fraying of ends. These might be fine and are unlikely to
> affect your free energy if they are not close to the ligand.Also, the RMSD
> for the complex does reach a plateau around 4-5A about halfway through. You
> cannot tell, though, if the structure has stabilized because it may still
> be chaning conformation but staying 5A from the reference. I prefer taking
> RMSD to the final structure (or better, to a cluster representative, if you
> can do that analysis). Then use that as the reference structure for RMSD
> and see if the RMSD values are low for the second half with respect to that
> structure.
>
> Overall the issue is that these RMSD plots do not give enough information
> to know if the system is behaving well or not, since we don't know much
> about what you are simulating and how you are calculating the RMSD values.
> I think it's best not to use broad measures like overall RMSD, but to use
> your knowledge of the system to analyze specific properties and see if they
> are reasonable (for example, DNA helical properties, ligand-DNA hydrogen
> bonds, and so on).
>
> On Sat, Feb 20, 2021 at 9:34 PM Delwakkada Liyanage, Senal Dinuka <
> sdd313.msstate.edu> wrote:
>
> > Hello Dr. Foley,
> >
> > Yes, the simulations were done in the NPT ensemble. I looked at the
> energy
> > plots and it seemed to me that the energy convergence is attained. Below
> is
> > the attached snapshot of total energy vs simulation progress plot. Also,
> as
> > Dr. Simmerling suggested I looked in to the rmsd of the ligand, and the
> > ligand was stable throughout the last 100 ns of simulation time (image
> > attached). Nevertheless, I thought of extending my simulation time to
> > another 100 ns due to previous fluctuations in the complex rmsd.
> >
> > [cid:355520f2-ea0b-4298-8278-ed731b561041]
> >
> > [cid:785d16f5-99fc-4d41-b210-bcd7636d70c1]
> >
> > Thank you
> >
> > Senal Liyanage
> > ________________________________
> > From: Lachele Foley <lf.list.gmail.com>
> > Sent: Saturday, February 20, 2021 3:30 PM
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] Sufficiently equilibrated or not
> >
> > With RMSD, the issue might be more about convergence than
> > equilibration. But, you're certainly not ready for TI.
> >
> > Which ensemble are you in? Is it NPT? If so, what does your total
> > energy plot vs simulation progress look like?
> >
> > On Sat, Feb 20, 2021 at 2:58 PM Delwakkada Liyanage, Senal Dinuka
> > <sdd313.msstate.edu> wrote:
> > >
> > > Hello Dr. Foley,
> > >
> > > Thank you very much for your valuable input.
> > >
> > > Senal Liyange
> > > ________________________________
> > > From: Lachele Foley <lf.list.gmail.com>
> > > Sent: Saturday, February 20, 2021 1:55 PM
> > > To: AMBER Mailing List <amber.ambermd.org>
> > > Subject: Re: [AMBER] Sufficiently equilibrated or not
> > >
> > > It's due to the rising nature, mostly. But, you also need stable
> > > fluctuations. That is, if you have a significant change in the
> > > amplitude of the fluctuation or if there is a trend (rising or
> > > falling) in the data, then the system is not equlibrated.
> > >
> > > On Sat, Feb 20, 2021 at 2:46 PM Delwakkada Liyanage, Senal Dinuka
> > > <sdd313.msstate.edu> wrote:
> > > >
> > > > Hello Dr. Foley,
> > > >
> > > > Thank you for your feedback. If I may ask, is that due to the rising
> > nature of rmsd or rapid fluctuations of the points?
> > > >
> > > > Senal Liyanage
> > > > ________________________________
> > > > From: Lachele Foley <lf.list.gmail.com>
> > > > Sent: Saturday, February 20, 2021 1:41 PM
> > > > To: AMBER Mailing List <amber.ambermd.org>
> > > > Subject: Re: [AMBER] Sufficiently equilibrated or not
> > > >
> > > > I would not consider the system in that image to be equilibrated.
> > > >
> > > > On Sat, Feb 20, 2021 at 2:17 PM Delwakkada Liyanage, Senal Dinuka
> > > > <sdd313.msstate.edu> wrote:
> > > > >
> > > > > Dear Amber Users and Developers,
> > > > >
> > > > > Here I have attached is a rmsd plot obtained for a ~100 ns
> > equilibrated trajectory (saved at every 10 ps) of a DNA/ligand system. I
> am
> > attempting to calculate absolute binding free energy through a
> > thermodynamic integration (TI) approach. I was hoping if you could
> clarify
> > to me whether the system is equilibrated enough to proceed with the TI
> > calculations. I was under doubt due to the fluctuations shown throughout
> > the last 6000 frames (60 ns). I understand there isn't an exact answer to
> > this. But I appreciate your opinion on this.
> > > > > [cid:f8200194-9003-4107-accf-086dd0f15353]
> > > > >
> > > > > Thank you
> > > > >
> > > > > Senal Liyanage
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > >
> >
> http://secure-web.cisco.com/116hL3r26c60Pja8rn_aYFWEm7xUTHXaZuKnMzMO7EeTnyrUrIjWOChCXCV4tzsu9b670bcf4lJMFhcJx8DtrtoCKNvzMA9U_1l3OQnAE5ZIbVojX2uNG9PGBLKlm6I7sswRsWwO337AMzdK7070amGhn7CsrHDVUQ3YPBcZAArNxm2mTaKbv3RyFFvKnWiEwDB5nF3HJ3CI79UIRTKh25CT1MfW86LhFw4CuiH0VK3nPYRhUGs8ZiV1P4TdJhMnO9C75M4yctjzmP9fKYnd_lJS-Q4czdX9Rsj4VaS_meUiQLk6GIsLImCMY9dFfwO6e/http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber
> > > >
> > > >
> > > >
> > > > --
> > > > :-) Lachele
> > > > Lachele Foley
> > > > CCRC/UGA
> > > > Athens, GA USA
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > >
> >
> http://secure-web.cisco.com/116hL3r26c60Pja8rn_aYFWEm7xUTHXaZuKnMzMO7EeTnyrUrIjWOChCXCV4tzsu9b670bcf4lJMFhcJx8DtrtoCKNvzMA9U_1l3OQnAE5ZIbVojX2uNG9PGBLKlm6I7sswRsWwO337AMzdK7070amGhn7CsrHDVUQ3YPBcZAArNxm2mTaKbv3RyFFvKnWiEwDB5nF3HJ3CI79UIRTKh25CT1MfW86LhFw4CuiH0VK3nPYRhUGs8ZiV1P4TdJhMnO9C75M4yctjzmP9fKYnd_lJS-Q4czdX9Rsj4VaS_meUiQLk6GIsLImCMY9dFfwO6e/http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber
> > > >
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> > > > AMBER.ambermd.org
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> http://secure-web.cisco.com/1nYcGarqXbx_X59IqL9sLgdETxc9asWQp1ph2TDPhoZNtf8MLpuKstvTAL3tvlduRQFHc6_7TAB038IzCcxgqGOFzbmviUVmN9Xjt_-sx1zlCDnDRw-QVRRam3kes3N2lfV4NUlqAESRpBP7Dm9hmtBPtrFCH3NGddauxNM0PpVwkX_5gnhBSPeF3JICpfuYIXQv_AdP2CeU4Y0IOfhUavyGnFg1mOuI6YyvLP7CaqZIE4b9x1t2ubP3qpFahX_T8NBkXFcZPGTF0m8ZDRlSe7XydLkO0IfCNv5WQaCYq-OnMHNWk8Kg8kqYm_RcP6gVR/http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber
> > >
> > >
> > >
> > > --
> > > :-) Lachele
> > > Lachele Foley
> > > CCRC/UGA
> > > Athens, GA USA
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > >
> >
> http://secure-web.cisco.com/1nYcGarqXbx_X59IqL9sLgdETxc9asWQp1ph2TDPhoZNtf8MLpuKstvTAL3tvlduRQFHc6_7TAB038IzCcxgqGOFzbmviUVmN9Xjt_-sx1zlCDnDRw-QVRRam3kes3N2lfV4NUlqAESRpBP7Dm9hmtBPtrFCH3NGddauxNM0PpVwkX_5gnhBSPeF3JICpfuYIXQv_AdP2CeU4Y0IOfhUavyGnFg1mOuI6YyvLP7CaqZIE4b9x1t2ubP3qpFahX_T8NBkXFcZPGTF0m8ZDRlSe7XydLkO0IfCNv5WQaCYq-OnMHNWk8Kg8kqYm_RcP6gVR/http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
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> >
> http://secure-web.cisco.com/1pH31Gockmoi_e7miSy2KRwpLsRBlztgTj93vqsvHQemb67xixbWlEQfMIKdjxeNu0iq9wlFYcWR6FwI7XRZWRAnPSTLYL17ZBx56Jxkt63SNVS9elmmOOhFLinhCrkwpQOMbfC-HOs8T-DHUv8-xOV5w6v_zvwvCBecjHPHKa4Wu-wOmPr8ZMSdi67dR9vFe3NJjWi8SFAgLrDvOGRJlu-nEXOMYQTgwfcANdCCCacZhrwLaG1GrFHg6qfyCwV0ODZaCbV6Z0ocIimcNw6fXx61CqspvzdiRdpaZvjDeeGkEQ-uyYywr_NjrrT8eF0lF/http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber
> >
> >
> >
> > --
> > :-) Lachele
> > Lachele Foley
> > CCRC/UGA
> > Athens, GA USA
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> >
> >
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Received on Sun Feb 21 2021 - 09:00:02 PST
