Yeah, 2.1 cents. Also, I forgot to mention that a single hydrogen
bond of about 1kCal (e.g. protein to ligand) can cause an RMSD
change by an 1A. That may not be common knowledge.
BTW I do agree with the referencing and tumbling comment in the
RMSD, but was thinking about H-bonds and overall motion. Looks
like RMSD is protein-ligand complex and just ligand in the green line?
Gordon Chalmers
________________________________
From: Gordon Richard Chalmers <gordoncs.uga.edu>
Sent: Sunday, February 21, 2021 11:12 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Sufficiently equilibrated or not
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
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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
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>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
>
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Received on Sun Feb 21 2021 - 09:30:02 PST
