Molecular dynamics (MD) is an approach used for simulating dynamic processes through successive integration of Newton's equations of motion.
Questions tagged [molecular-dynamics]
354 questions
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How does a knife cut things at the atomic level?
As the title says. It is common sense that sharp things cut, but how do they work at the atomical level?
wtoh
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When I put my hand on a hot solid why don't the particles transfering heat to my hand exert a force on it?
When I put my hand on a hot metal (say) solid, I can feel my hand heating up. I suspect this is caused mostly by particles (electrons, atoms, ...?) from the solid colliding with the particles that make up my hand thereby transferring kinetic energy…
Damian Birchler
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Why aren't Runge-Kutta methods used for molecular dynamics simulations?
One of the most used schemes for solving ordinary differential equations numerically
is the fourth-order Runge-Kutta method. Why isn't it used to integrate the equation of motion of particles in molecular dynamics?
WedgeAntilles
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30
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When I stretch a rubber band, it breaks. When I hold the broken ends together, why doesn't it join again?
The question is simple. When we join the two broken surfaces, what is it that keeps the surfaces from connecting with each other, while earlier they were attached to each other? Also, would the two sides join again if I hold them together for an…
Prem
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How can fast moving particles gain energy from slow moving ones?
Imagine a large diameter piston filled with water connected to a small funnel. When you press on the piston slowly but with considerable force the water will move very quickly from the funnel in form of a jet. But how is it possible on a molecular…
Ardath
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Is there such a thing as a "physical" fractal?
The recent discovery of a molecule that mimics the Sierpinski gasket has spurred headlines identifying it as the first fractal scientists have found in nature. I find these claims highly dubious because it's either entirely impossible for a real…
starseed_trooper
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19
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Does there exist a free good molecule / atom simulation software?
I'm looking for a software or software package (for example C/C++) that can simulate a lot (say thousands at least) of molecules in action (ie. in movement or attached to say static walls).
I have found several but they seems to be either 'gas…
Valmond
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Do Franck-Condon oscillations have natural lineshapes?
I recently found a paper (for the curious, this one) that talks about observing the motion of a nuclear wavepacket in H2O, as initiated by tunnel ionization. This wavepacket should be thought of as a superposition of the different vibronic states of…
Emilio Pisanty
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Why isn't the Gear predictor-corrector algorithm for integration of the equations of motion symplectic?
Okumura et al., J. Chem. Phys. 2007 states that the Gear predictor-corrector integration scheme, used in particular in some molecular dynamics packages for the dynamics of rigid bodies using quaternions to represent molecular orientations, is not a…
F'x
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Can we fully simulate molecular physics?
Is our knowledge of physics complete enough to achieve fully natural simulations of molecular interactions in a computer simulation? How far off are we?
Reason for question: I wonder how far we are from simulating cells in a computer. I assume that…
eric
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When two molecules collide, does it produce a sound?
When we are in an empty room with no one around, we don't hear any sound, but there are billions of atoms and molecules that are colliding at the same instant.
So my question is, when two molecules collide, does it produce a sound?
Preet
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What is the "direction" of the transition dipole moment? (Understanding Eq. 9.29, Charge and Energy Transfer 3rd Ed, May & Kuhn)
For a real vector $\mathbf{r}$, the direction is given by: $\hat{\mathbf{n}}=\mathbf{r}/\left|\mathbf{r}\right|$.
The transition dipole moment is a complex vector. How do you define its direction?
The point of this question is that I am trying to…
a06e
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12
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Born-Oppenheimer separation in Dirac bra-ket notation
Most derivations I have seen of the Born-Oppenheimer approximation are made using wave-functions. To understand it better, I was trying to write a derivation using Dirac notation, but I am stuck. I am going to post what I have done so far so you…
a06e
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Why is the canonical ($NVT$) ensemble often used for (classical) molecular dynamics (MD) simulations?
Molecular dynamics (MD) simulation is a common approach to the (classical) many-body problem. It relies on integration of Newton's equations of motion to simulate the trajectories of many (e.g., ~1,000-100,000) particles.
In my limited exposure to…
Andrew
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Deuterium density in seawater
I heard today that deuterium for nuclear fusion could be extracted from the Oceans, in which it is present in "heavy water." I heard this claim:
"Deuterium is distributed uniformly with Ocean depth."
This contradicted my naive expectation that…
innisfree
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