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

From: David A Case <>
Date: Wed, 16 Sep 2020 08:59:05 -0400

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


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Received on Wed Sep 16 2020 - 06:00:04 PDT
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