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EDIT: Apparently this is called reactive molecular dynamics. It seems that the ReaxFF potential function is used for some reactions like this.

I am interested in adding support for reactions to a coarse grained molecular dynamics simulations. On the whole each particle will represent a large biomolecule.

Most of the literature I have surveyed indicates that the force fields used in molecular dynamics make it unsuitable for modelling reactions (as in determining if a reaction will take place). For my simulation I don't think that I need to determine if it is electronically/energetically possible for it to occur. I want to simulate rule-based reactions.

I have seen one book where the author says that with prior knowledge it is possible to assume that if two particles in your simulation collide they will react.

1) Is this correct? If so, what would one need to know about the particles? I know that Na$^+$ and Cl$^-$ react to form NaCl. Could I just detect if they collided and then replace them with an NaCl simulation particle?

2) Would this work with large molecules (one simulation particle per molecule)? If I knew that enzyme A acted on substrate B to produce substrates C and D (A+B$\rightarrow$A+C+B), then if I detected a collision in my molecular dynamics simulation would it be scientifically correct to perform the reaction?

3) What prior knowledge would I need for this to work? Is this the sort of knowledge that is readily available? (I.e. A+B$\rightarrow$C 50% of the time)

4) Is this good science? Is it unlikely that a simulation of a biological system using this rule based technique would get published in a good journal?

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  • $\begingroup$ I'm not an expert on MD, but I would venture it depends on the type of reaction. For example, an N2 and O2 colliding under room-temperature conditions certainly wouldn't react -- they would need enough kinetic energy to transfer enough energy to the vibrational modes that the molecules came apart. Then the parts would have to collide again to form NO or NO2 etc.. But something like Na+ and Cl- could reasonably be assumed to react if collisions occur; unless they had so much kinetic energy that they didn't stick together. $\endgroup$
    – tpg2114
    Commented Aug 9, 2013 at 18:39
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    $\begingroup$ Have you googled for reactive force fields? See e.g. here: en.wikipedia.org/wiki/ReaxFF $\endgroup$
    – Johannes
    Commented Aug 9, 2013 at 18:39
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    $\begingroup$ Note your enzyme would work as A+B$\rightarrow$A+C+D. $\endgroup$
    – Emilio Pisanty
    Commented Aug 9, 2013 at 18:44
  • $\begingroup$ @Johannes I have encountered ReaxFF and considered asking about it, but thought I was waaay of course. Apparently what I want to do is called reactive molecular dynamics $\endgroup$
    – RNs_Ghost
    Commented Aug 9, 2013 at 18:47
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    $\begingroup$ Regarding Na / Cl, they are not binding by covalent means so their (often intermittent) binding is indeed modeled by MD forcefields. Creating salt-crystals or similar is probably not what the ff parameters is optimized for though. $\endgroup$
    – BjornW
    Commented May 30, 2015 at 23:12

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Ok so this is a over a year later, but no answer yet so here goes.

One approach would be to use a Boltzmann type/Arrhenius type approach to collisions to see if they lead to reaction.

So you could figure out a probability of reaction, $p$, which would be equal to $1$ if the reaction is 'Exothermic' (where energy is released) or equal to

$p=e^{-{\Delta E \over kT}}$

where $\Delta E$ is the energy required for reaction to occur if it is endothermic (where energy is required).

This would be crude, but somewhere to start.

You could look up RRKM theory and QET and other things in reaction dynamics to get beter insight as to what to do.

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