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In molecular dynamics simulations you apply and solve Newton’s equations of motion for a set of atoms to obtain real dynamical information on how individual atomic positions change as a function of time.

Why can't this same method be used to determine atomistic mechanisms via which chemical processes occur? Is it because the length of time which you run simulations isn't long enough? Also what difficulties are there with solving these equations numerically in MD simulations ?

Im confused on these points.. Any help would be appreciated. Thanks

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  • $\begingroup$ I think forces in atomic scale can not be modeled classically and time scale problem is also important. Because the time step should be from the order of fs(1E-15 second) in atomic scale and many time step needed to model the system. $\endgroup$
    – Abolfazl
    Commented Oct 31, 2015 at 7:29

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You're essentially right, it's difficult (impossible if you're doing it quantum mechanically) to run a molecular dynamics simulation on the timescale of a chemical reaction. There are two reasons for this: the first is that in any system that is large enough to ignore finite size effects, there will be a huge number of degrees of freedom, so the system will either need to be very carefully initialised (impractical), or you will need to wait for the atoms to be at the right place in the right time. The second is the activation barrier (excluding barrierless reactions): unless you are running the simulation at an unrealistically high temperature, reaction events occur at a very low rate, and you would either need a huge system (computationaly expensive) or a long time to witness them.

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To describe a chemical reaction first you have to define a model, for example, in a reactive collision like A + BC -> AB + C you could use as a first approximation the transition state theory (TST) and perform the determination of the physical observables with some methodology like the quasi-classical trajectories (QCT), which solves the Langrange's equations of motion (a set of differential equations solved by RK4, for example) and perform some artificial quantizations to include the quantum-mechanical effects on the system. You can use the classical newtonian ideas (or more precisely, Hamilton o Lagrange's ones) and extend it with artificial quantizations.

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