Re: [AMBER] expected average fluctuations in amino acid covalent bond distances, angle and torsion during typical md simulations

From: Vaibhav Dixit <>
Date: Wed, 16 Sep 2020 21:09:41 +0530

Dear David (and Amber community),
Thanks a lot for insightful comments, I will surely try these out and read
the paper.
Moving one step forward with your response is it then possible to estimate
Marcus parameters e.g. reorganization energies from MD simulations for
protein redox states with MD simulations using Amber/AmberTools? I'm
assuming that such an analysis even if technically feasible might be too
tedious and then lack accuracy due to some of the factors you mentioned in
addition to the inner/outer sphere reorg. Es that need to be estimated.

One, not very old, study in JACS is using Amber towards this end (
They explained many complexities and also did QM/MM to estimate reorg. Es,
but I don't have an understanding if current MD methods (used alone) are
suitable/accurate for the same. Probably not, mainly because the
current-standard force fields (e.g. ff14sb) don't model the bond/angle
vibrations as accurately as required for Marcus parameters, do you expect
the ff19sb <>to be
better at this.
Also, if I understood correctly, the cellulose IR spectra example a
non-protein system and thus doesn't address my query about IR spectra of
proteins from MD simulations.
I know I have to search/read a lot to fully understand the current
state-of-the-art in these areas and to be able to meaningfully use
Amber/AmberTools towards this end.
Nonetheless, I will be grateful and appreciate valuable suggestions and/or
tips that you and the list can give me in this regard.
It might also help others trying to begin work in this area or are just
interested to learn more on the topic.
Thank you very much and best regards.

On Wed, Sep 16, 2020 at 6:29 PM David A Case <> wrote:

> On Wed, Sep 16, 2020, Vaibhav Dixit wrote:
> >
> >I think a typical force field will cause large energy changes if bond
> >distances, and angles vary significantly from the average/equilibrium
> >values during a typical room temperature MD simulation. Thus if I try to
> >plot variations in these parameters as a function of the number of MD
> >steps, I won't see much variations, is this correct?
> Depends on your definition of "much". Why don't you try it and see?
> Save snapshots are very frequent intervals (say every step for a short
> simulation, perhaps even with dt=0.001). You can see the bonds vibrate.
> >I haven't seen MD simulations being used to estimate IR Spectra
> You should search harder, as this has been done. It's not all that
> popular for looking at bond vibrations, since other methods (like quantum
> chemistry) are more accurate, and nuclear quantum effects can also be
> important. But it certainly can be done: just take the Fourier transform
> of the dipole moment vs. time.
> One paper I like, concentrating on condensed phase systems, is this one;
> it gives a good overview of the basic theory involved.
> %A V. Agarwal
> %A G.W. Huber
> %A W.C. Conner, Jr.
> %A S.M. Auerbach
> %T Simulating infrared spectra and hydrogen bonding in cellulose I`beta`
> at elevated temperatures
> %J J. Chem. Phys.
> %V 135
> %P 134506
> %D 2011
> ....dac
> _______________________________________________
> AMBER mailing list

Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
Assistant Professor,
Department of Pharmacy,
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
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Received on Wed Sep 16 2020 - 09:00:03 PDT
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