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

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Wed, 16 Sep 2020 00:27:54 +0530

Dear Amber community,
I didn't get relevant hits from a Google search on the subject topic, thus
I'm asking this question here. My query is as follows,

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?
If this is the case, then the next question is, does this represent real
proteins in solution.
I guess not, because bonds and angles in proteins do vibrate at room
temperature and thus can be IR active.
Same seems to be true for ligands modelled by gaff force field.
If one expects to see significant variations, do different proteins show
differences in such parameters? What about metalloproteins and ligands?

I'm assuming that torsions are expected to be more flexible at room
temperature and force fields are trained to model this fact. I haven't
seen MD simulations being used to estimate IR Spectra, that suggest that
probably during MD simulations bonds and angles are effectively fixed.
But I'm not sure if I'm thinking right here.
Please help me understand this aspect by sharing your thoughts and expert
If possible please redirect to any relevant literature/book on the topic.
I look forward to receiving insightful comments and suggestions.
Thank you very much in advance.
Best regards
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Received on Tue Sep 15 2020 - 12:00:03 PDT
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