# Tagged Questions

Molecular dynamics (MD) is an approach used for simulating dynamic processes through successive integration of Newton's equations of motion.

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### Molecular dynamics and detailed balance

In developing methods to perform Monte Carlo simulations one sufficient condition to preserve the stationarity of the target probability distribution is to impose detailed balance i.e. [Gardiner page ...
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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 ...
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### Moment of inertia of rotating particles in center of mass frame?

I am trying to simulate a collision between two molecules. I know the energy for every position/orientation, from which I can calculate the forces. The treatment is classical and the molecules are ...
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### Thermionic emission, delayed emission and predissociation

In molecular photodissociation, the thermionic emission, delayed emission and predissociation are the same? Otherwise, what is the difference between them? My question is not about the solids, but I ...
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### Forces from molecular potential energy surface

Let's assume we cannot use Hellmann-Feyman theorem and we wish to calculate the forces on molecules' atoms at arbitrary configuration only from its potential energy. My question is how many different ...
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### Generallized Canonical Ensemble - Isobaric Ensemble

I am trying to understand the way generalized canonical ensembles like the pressure ensemble are derived from the standard canonical ensemble. In the derivation for the standard form, one defines a ...
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### Reaction coordinate as a function of atomic positions

I'm going over some (molecular dynamics) related literature - specifically the derivation of the Weighted Histogram Analysis Method (WHAM). As a quick backdrop WHAM is a method for stitching ...
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### How to explain the momentum exchange of two solid particles collision at molecular scale?

Here is my question: assume two solid sphere collided to each other in vacuum, at macroscopic, it can be explain by Newton's law. But at molecular scale, does the surface atoms touch to each other or ...
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### What actually makes boiling happen?

Boiling can be breezed over easily with a few rudimentary diagrams and a couple equations, but I seek a deeper explanation. The definition of boiling is that the vapor pressure in the liquid is ...
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### Force field for calcium ions, potassium ions and water in molecular dynamics

I want to adapt my existing MD simulation so that it can handle these three species. For the interactions of the ions I thought that I would use the coulomb potential, but I don't know what sort of ...
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### reactions in molecular dynamics simulations

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 ...
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### Viscosity calculation of a rarefied gas

I am studying the rotational-translational relaxation of a diatomic gas (like oxygen) using a GPU in order to accelerate the calculations; during the calculations I get the translational temperature, ...
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### 2D slab model for LJ potential

I have a program implementing a LJ(Lennard-Jones) molecular Dynamics(MD) simulation with isokinetic thermostat. I want to modify that program to study the phase characteristics of LJ particlesin 2D ...
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### Notation of a vector containing equation in a paper

I'm trying to implement Coulomb long range interactions into a molecular simulation program using a particle-particle/particle-mesh Ewald solver. The following equation from the paper "How to mesh up ...
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### Time Scales Of Processes In Molecular Dynamics

Suppose I run a molecular dynamics simulation of a fluid sandwiched between solid walls which are periodic in the lateral directions and finite in the direction of the fluid film thickness. Now, I ...
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### How strong is the HCN Union when modelling with springs

I'm modeling the HCN Molecule with springs, giving the bounds between H and C the name k1 and between C and N k2. Is there any information of how strong is the bound? We were asked to get the ...
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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 ...
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### FCC-to-BCC phase transition in NaCl, Buckingham or Lennard-Jones potentials?

Background The transformation from B1 (face centered cubic (FCC) type) to B2 (body centered cubic (body centered cubic (BCC) type) structures is one of the best documented high pressure phase ...
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### Atomic Stress (Virial Stress) and Harmonic Springs

The general context here is polymer physics. The stress tensor in a bead-spring simulation can be easily computed using the Virial Stress (which may be named the Kirkwood formula, or the Doi-Edwards ...
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### What is thermophoresis?

I read wikipedia article and I saw a bad youtube presentation on thermophoresis, however I don't have a clear insight about the subject. I assume the forces are basically Brownian molecular forces ...
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### Two Particles in a Harmonic Oscillator with repulsive short-range potential

Do bear with me, I am attempting to learn to write some simulations on the computer and learn some simple MD, so I defined sort of a toy problem. I have two particles confined in a Harmonic Potential ...
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### Molecular Dynamics (MD) Simulation: energy fluctuations in NVE ensemble

I'm writing my first MD simulation (ever) for liquid Argon. The code is up and running. I am supposed to do the calculations in the NVE ensemble. Having implemented a 4th order symplectic integrator (...
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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 ...
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### Good book for learning fluid statistics

I'm currently using Gray and Gubbins Theory of Molecular Fluids to learn about the statistical physics of fluids. It may be a fine reference text, but I'm not impressed with it as an introduction to ...