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

learn more… | top users | synonyms

0
votes
0answers
17 views

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?
1
vote
3answers
42 views

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' ...
0
votes
2answers
73 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 ...
0
votes
0answers
15 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 ...
0
votes
1answer
10 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 ...
0
votes
1answer
12 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 ...
1
vote
2answers
42 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 ...
0
votes
0answers
29 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 ...
0
votes
0answers
33 views

absorption and reflection of sound on molecular level

Can someone explain the reflection and absorption of sound on the molecular level? What really is reflection? Why porous and soft material absorbs sound? What's the definition of soft in terms of ...
0
votes
0answers
53 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 ...
1
vote
0answers
20 views

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 ...
1
vote
1answer
67 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 ...
0
votes
1answer
46 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)?
1
vote
0answers
33 views

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 ...
2
votes
0answers
40 views

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: $$ ...
1
vote
1answer
44 views

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 ...
2
votes
1answer
77 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?
0
votes
2answers
57 views

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 ...
0
votes
1answer
95 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, ...
2
votes
1answer
41 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 ...
0
votes
1answer
54 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 ...
0
votes
0answers
49 views

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 ...
0
votes
0answers
45 views

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 ...
0
votes
0answers
16 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 ...
1
vote
1answer
68 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 ...
0
votes
0answers
21 views

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. ...
0
votes
0answers
29 views

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). ...
0
votes
0answers
101 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, ...
0
votes
1answer
35 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 ...
0
votes
0answers
40 views

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 ...
117
votes
3answers
11k views

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?
0
votes
1answer
99 views

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 ...
0
votes
0answers
30 views

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?
1
vote
1answer
1k views

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 ...
1
vote
0answers
202 views

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: ...
0
votes
2answers
175 views

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 ...
18
votes
5answers
3k views

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 ...
1
vote
0answers
121 views

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 ...
1
vote
0answers
82 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 ...
2
votes
3answers
68 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 ...
1
vote
1answer
157 views

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 ...
4
votes
1answer
320 views

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 ...
2
votes
1answer
603 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 ...
1
vote
0answers
82 views

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, ...
3
votes
1answer
154 views

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 ...
0
votes
0answers
66 views

Can peridynamics give accurate quantitative results?

I'm applying for a position that is interested in studying crack growth using peridynamics. I have experience with MD on polymeric systems, but I had never knew of this method before. It seems very ...
6
votes
0answers
419 views

Surface tension between water (liquid) methane (gas)

In my project I should calculate surface tension between water and methane with lammps. I write the program.I use SPC model for water and $l_j$ for methane and water - methane. But now I don't know ...
0
votes
2answers
1k views

Does the Lennard-Jones force equation give its answer in Newtons?

I'm trying to do the dimensional analysis of the Lennard-Jones force to work out what units are being used in my MD simulation. The lennard Jones force is given as the negative derivative of the ...
1
vote
1answer
109 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 ...
9
votes
1answer
182 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 ...