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

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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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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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Gases Expanding Vacuum

Why do gasses expand in space rather than attract forming a liquid? Do some gasses attract when they are colder?
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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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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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70 views

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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29 views

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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134 views

Requirements to study molecular simulation

I'm intending to learn some basic concepts about molecular simulation, but I have not had Classical and Quantum Mechanics classes yet, then I'd like to know if those Susskind's books called "The ...
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37 views

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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92 views

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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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 ...
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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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80 views

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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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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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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124 views

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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Symmetry in program for ewald summation

The formula for Ewald summation as given in Allen and Tildesley - $$ U = U^{(r)} + U^{(k)} + U^{(bc)} + U^{self} $$ where the k-space contribution of potential is given by $$ U^{(k)} = \frac{1}{\pi ...
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37 views

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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98 views

Langevin Equation - Stochastic Differential Equation. What are the subtleties?

I am trying to find out the motion of a particle in 3D governed by the Langevin equation, numerically. Anyway, the Langevin equation is given by $$m \ddot{x} = -(6\pi a\nu) \dot{x} + F_b $$ where ...
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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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64 views

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 ...
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62 views

Calculating atomic forces from total force and torque on molecule in molecular dynamics (MD)

I guess this problem applies to any body that is composed of a small number of particles, but for the sake of simplicity and concreteness, let's consider a classical model of a molecule consisting of ...
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54 views

Lennard Jones Total system energy [closed]

i am trying to implement/extend an implementation of Lennard-Jones potential simulation regarding Xenon molecules (for curious ones, the code can be found here functions (force_naive->lj_force)). ...
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Using reflective optics concepts to focus gas pressure in a vacuum

At very low vacuum pressures the bulk behaviour of molecules can be approximated by non interacting particles bouncing off of the chamber walls: For an monotonic molecule such as He with perfect ...
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Is there any way I can tell whether increase in total energy in molecular dynamics simulation is due to large time step or not?

Does increase due to large time step has any type of signature that will tell for certain (or almost certainly) that that is the reason?
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Why is intermolecular potential energy given in 'per mole'?

I was just wondering that if intermolecular potential is the interaction potential energy of two atoms/molecules, then why do we give its value in J/mole? I don't understand why 'per mole' ...
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155 views

Which units should I use in molecular dynamics simulation?

I have written a simple molecular dynamics simulation program. The simulation runs fine but the physical properties (in particular, I have calculated temperature) are off by many scales. I understand ...
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59 views

Incoherent Intermediate Scattering Function from Molecular Dynamics Simulations

I want to calculate the incoherent intermediate scattering function (ISF) using the self-part of the van Hove function. When I plot the ISF as a function of time, should I consider the modulus of the ...
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What is the potential associated to a pure torque proportional to one of the principal axis of a particle?

I'm writing a code in molecular dynamics in which a particle is subject to a pure torque around one of its principal axis. E.g., if the particle has principle axis $\hat u$, $\hat v$, $\hat f$, all ...
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35 views

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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87 views

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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30 views

What exactly is cutting with a knife will look like on the atomic scale? [duplicate]

Some times I like to view the world in the microscopic scale .ie. at this level all objects any thing will be collection of atoms which we normally don't view with our naked eye. At that scale I ...
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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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Doubt about Hard Sphere Model

I couldn't find a proper answer about this question: if I have a gas formed by a single species (ex: biatomic gas like O2), what is the diameter $\sigma$ of the relative hard sphere model? Is it the ...
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91 views

Molecular simulation applied to astrobiology

There is some research group which use molecular dynamics simulations to study the origin of life according to the hypothesis of abiogenesis? I'm just beginning to know this subject so I don't know ...
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NVT simulation of the phase transition

Why it is assumed to be incorrect to simulate,say, liquid-solid transition at constant volume (NVT simulation)?
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Why is it inappropriate to calculate free energy change from end points alone?

In molecular dynamics, free energy changes are estimated using a variety of protocols to establish a path between the starting and ending states. The classic example is umbrella sampling in which a ...
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How can the fictitious mass in the Car-Parrinello method reproduce the “real” dynamics?

In the Car-Parrinello method, to solve simultaneously the classical equations of motion for the atoms and the Kohn-Sham equations for the electrons, the following effective Lagrangian is used: $$ ...
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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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132 views

Time length molecular dynamics

What limits time length of simulation in molecular dynamics to femto and in coarse graining to nano or micro second?
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Is there such a thing as an interaction radius for molecules?

My question is about estimating the radius of influence between two molecules; picture some mixture, comprised of water, oxygen gas (in small concentrations) and a molecule we denote $G$. In the ...
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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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Mass scaling in molecular dynamics

I've noticed some authors scale the mass of particles in molecular dynamics simulations while leaving the force field parameters the same in order to achieve materials of different densities. Does ...
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How introduce sound wave in molecular dynamics or dissipative dynamic particles?

How could I introduce sound wave in molecular dynamics or dissipative dynamic particles? What do specify which is applicable between molecular dynamics and dissipative particle dynamics? problem is ...
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Need to Zero Angular Momentum

I'm writing a molecular dynamics simulation and need to zero the angular momentum of a collection of particles. For each particle I know the location, mass and velocity. My rotational physics is a ...
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81 views

Is there any physical simulator precise to atomic levels and quantum effects? [duplicate]

There are tons and tons of physics simulators for classical/large scale physics. I'm interested in a simulator in which you feed an input as atoms and positions and it simulates the evolution of the ...
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154 views

Solution to a kinetic temperature problem

I have a particular equation that needs to be solved for the kinetic temperature of a stream of gas particles. If we let the kinetic temperature be designated by the letter x, the equation becomes, ...
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39 views

Applying the time evolution operator as a form of molecular dynamics

I had a kind of weird idea. In molecular dynamics, long timescale simulations (like protein folding) are a really hard problem because you can't "skip steps" of the simulation without huge ...
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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?