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

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MD simulations and sputtering

can someone recommend references to study for a newbie in molecular dynamics simulation? what is sputtering in MD simulations.
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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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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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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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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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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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27 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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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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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 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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64 views

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); so here is my question: How are these two fields ...
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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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1answer
74 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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53 views

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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1answer
88 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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112 views

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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how to find the frequency in a auto correlation function?

I am running some molecular dynamics simulation with carbon nano tubes and calculating the velocity auto-correlation function (VACF). Each 10 time steps is writen in a file the VACF and in the final ...
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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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What is the temperature effect on trajectories in phase space in molecular dynamics?

In molecular dynamics simulations or microcanonical ensemble (fixed-energy), what is the effect of temperature on the trajectories of the reacting systems (let's say two reactants react to form two ...
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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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Pressure components in a film

I am performing molecular-dynamics simulations of a polymer near a crystalline substrate (polymer film). I am comparing the mechanical properties in the film with the properties in the bulk polymer. ...
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Tersoff parameters

I am studying the tersoff potential i am trying to understand the physical meaning for each parameters in this potential. The development of Tersoff potential is a little fuzzy (several articles). ...
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135 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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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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need some references in molecular dynamics simulation

I Just start we a new model on my project and I will need to work with Molecular dynamic simulation. I have to simulate dynamics of many filament inside a network (actomyosin network).The problem is ...
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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?
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Fock matrix elements for RHF formalism

Here I refer to a particular book Molecular Quantum Mechanics by Peter W. Atkins and Ronald S. Friedman, but similar derivation could be found in many other texts. So, when obtaining the explicit ...
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Verlet timestep

I am using velocity Verlet in molecular dynamics. Is just a simple question, if a simulation using time-step femtosecond, in velocity Verlet is just necessary $dt = 10^{-15}$ to use femtosecond?
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Understanding the mean square displacement in molecular dynamics

In a Molecular Dynamics (MD) simulation, the mean square displacement $\text{MSD}$ is given by $$\text{MSD}(\delta t) = \left\langle\left|\vec{r}(\delta t)-\vec{r}(0)\right|^2\right\rangle,$$ where ...
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Coherent Intermediate Scattering Function from Simulations

I want to calculate the coherent intermediate scattering function, $S_{\text{coh}} (\mathbf{Q},t)$, from a molecular dynamics trajectory, based on its definition. The definition of the function is: ...
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Molecular mean free path probability

Let's let $p(\xi)$ be the probability a molecule travels at least $\xi$ between collisions, lets say $\xi=0.01$. When I think of this statement, I think it it is the probability the molecule is able ...
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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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Correct way to include constant external force in virial and pressure calculation

Halo, given a simulation cell with N particles where particles interact only with bond and pair potentials and periodic boundary conditions (minimum image convention) are used. On a subgroup of ...
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Langevin equation

A molecule consists of two atoms whose centers are located at $\mathbf{r}_1$ and $\mathbf{r}_2$ respectively. The atoms are connected by a bond that can be approximated by a harmonic spring, so that ...
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Do molecular bounded systems shield or reduce neutron cross-sections?

When talking about neutron cross-sections, literature is usually investigating isolated cases of Neutron + Atom. Here, the abundance of hydrogen is dominating neutron fluxes through material. I ...
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Molecular rotation - Energy levels for an asymmetric molecule

For a molecule with spherical symmetry, the energy level of rotation for quantum number $J$ is: $$E(J)=\frac{J(J+1)\hbar^2}{8\pi^{2}I}$$ "$I$" is the Moment of inertia for the molecule ...
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Molecular dynamics: Thermostat via damping modulation

Molecular dynamics (MD) often use a thermostat so that they can control the temperature. Temperature tends to drift due to endo/exothermic reactions (that would normally absorb/emit heat to a large ...
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638 views

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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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, ...