# 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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### Maxwell-Boltzmann distribution in Lennard Jones units

I'm studying thermostats in Molecular Dynamics. A very easy way (and poor, but I don't care for the moment) to implement a thermostat is to randomize momenta at some steps. These new momenta are ...
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### Nose-Hoover Barostat

Much can be found about the Nose-Hoover Thermostat. However I seem to be having difficulty finding out details about the Nose-Hoover Barostat, and how it is implemented. Would anyone be able to give ...
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### Explicit solvent simulations in NVE ensemble: Molecular Dynamics

I am simulating a SDS micelle system in NVE ensemble at room temperature. I am not sure if the system is equilibrated, since the pressure variations are around 100's of atm, where the average pressure ...
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### Difference between molecular dynamics and direct simulation Monte Carlo

I just started studying about rarefied gases and I came across the concepts of Molecular Dynamics (MD) and Direct Simulation Monte Carlo (DSMC). My question is: How are these two fields related to ...
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### Thermostat in Dissipative Particle Dynamics

I'm doing a computational experiment about dynamics of a solvated line polymer, with dissipative particle dynamics(DPD). However when I try to measure kinetic temperature of the whole system(monomers +...
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### Relation between solvent accessibility and brownian motion

Assume one has a molecule (made of nodes) inside a solvent. If one tries to model the average effect of the interaction between the molecule and the solvent, one has two effects: 1- Friction term on ...
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### Calculating Microcanonical Entropy in Molecular Dynamics

As a beginning, I am simulating Argon liquid at 94 K and characterising as it is done by the Rahman's first paper on Molecular Dynamics. After going through the first two chapters of Art of Molecular ...
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### Any quadrupole approximation? Any example?

In atomic and molecular physics we quite often encounter with electric dipole approximation. The dipole approximation we do when the wave-length of the type of electromagnetic radiation which induces, ...
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### Deriving the change in the Helmholtz free energy in the context of the free energy perturbation method

I am reading Free Energy Calculations: Theory and Applications in Chemistry and Biology by Chipot and Pohorille. At the beginning of the text (page 19, for example), the authors define the Helmholtz ...
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### Why is the trajectory of the alpha particle in a cloud chamber almost straight?

This question baffled me since high school. Presumably, the alpha particle has collided with macroscopically large number of molecules when it makes a macroscopically large displacement. One would ...
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### What happens to the velocity map image if the plane of polarization is not on the plane of the detector?

In an electron Velocity Map Imaging (in Velocity Map Imaging in general) it is required that the plane of polarization to be parallel to the plane of the detector (in other words, plane or ...
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### Evaluation of width function; thermal neutron scattering cross section

I am attempting to perform some molecular dynamics simulation, based off of this paper, and do not have the slightest clue how they evaluate the width function (Eq. 4). My attempt at figuring it out/...
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### For molecular orbital, LCAO approximation is trusty?

I'm curious how the LCAO approximation is trusty. I'm majoring in physics and usually treat solid using tight binding method. Using tight binding method, We can think the periodic molecular orbital ...
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### Why is modelling water so difficult?

There are several models of water that have come into existence so far. Nevertheless, there is no one particular model which effectively gives all the properties of water correctly. A model like TIP3P ...
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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 ...
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### Setting up initial configuration of a Micelle - Molecular Dynamics

I have just started learning Molecular Dynamics using dl_poly_classic and analysing trajectory using nMOLDYN. Our primary aim is to do neutron scattering, but however we do Molecular Dynamics to ...
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### Calculation of long-range forces in Molecular Dynamics - Ewald summation

I am trying to write a code to calculate the potential and forces, for the same using ewald summation.For this purpose, the formula for potential and force I have used is :  U = U^{(r)} + U^{(k)} +...
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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 (...