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

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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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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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147 views

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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44 views

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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118 views

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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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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40 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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195 views

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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21 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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1answer
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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1answer
118 views

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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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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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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32 views

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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1answer
42 views

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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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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3answers
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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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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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2answers
94 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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26 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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3answers
71 views

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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1answer
11 views

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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16 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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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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61 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
73 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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436 views

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 ...
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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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1answer
61 views

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 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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Franck Condon Principle and Born Oppenheimer approximation

My question here is purely fundamental. I am confused with the concept in Franck Condon (FC) principle and Born Oppenheimer (BO) approximation. The FC principle is in accordance with the BO ...
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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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87 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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87 views

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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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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18 views

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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70 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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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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1answer
36 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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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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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 ...