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Questions tagged [molecular-dynamics]

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

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Molecular dynamics - Fermi Pasta Ulam Tsingou

I'm taking a course on computational physics, but still fairly new to physics at this level, and because of that, I'm looking for some help getting a better understanding of the following. Working on ...
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Do proteins interact through classical or quantum mechanics?

For the protein interactions that occur in our cells, do they "follow" classical mechanics or quantum mechanics when interacting? I have zero knowledge about quantum mechanics, but I was wondering ...
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In Molecular Dynamics calculation, do the laws of thermodynamics hold for all kind of ensembles?

I'm studying statistical mechanics with Reif's book. From the book, starting from the purely statistical view, all 0th,1st,2nd and 3rd laws of thermodynamics are derived, which I thought were axioms ...
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Modeling Atomic Motion

It seems in the molecular dynamics simulators that I've found thus far, most of them model the systems using models that treat nuclei and orbiting electrons as a single particle. At least, that's what ...
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Adjust PDF with Maxwell Boltzmann (Best Fit)

So I got a dataset consisting on different particle velocities. I've made an histogram (I'm using Octave/Matlab) and I also made the PDF. I'm not sure I've made the PDF correctly but these are my ...
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Creating a simulation of molecules

Just full disclaimer: I am a first year physics graduate student with very little experience in physics research. I would like to write to develop a toy model to teach myself a bit about spin ...
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How do I know that the time-step I'm using in my Verlet integrator is small enough?

I am performing a molecular dynamics simulation of a many-body system using the Verlet algorithm in an implicit solvent, i.e. adding noise to the equation of motion via a thermostat term. I want to ...
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Which bonds are broken when we use high laser energy?

If we suppose as in the picture that a laser with high energy been used to break down the bounds, what exactly happens? Is there anything to do with molecular orbitals? or?
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Radiation EIRP impact on organisms

I read some documentation about how harmless the non ionizing radiation can be and it looks like the arguments are around the frequency(hence the energy) of the wave. In the sense that a particle with ...
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51 views

Euler-Lagrange Equations for Molecular Dynamics

In the Car-Parrinello (CP) method for molecular dynamics simulation, the Euler-Lagrange equations are given as $$ \begin{aligned} \frac { d } { d t } \frac { \partial \mathcal { L } _ { \mathrm { ...
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How to explain pressure on a molecular level?

So when I'm on an airplane and I have a bag of chips, at some point when the pressure in the cabin lowers, the bag of chips will bulge up. Here’s how I’d explain this on a molecular level: There are ...
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Why do atoms repel when closer but attract when farther apart?

I was wondering why atoms, when pulled apart and then released, attract together, but I notice that there is a special distance at which this attractive force doesn't seem to act but rather those ...
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What are the possible method to simulate the dynamics of rigid bodies in simulation? [closed]

I just want to know the name of the methods, the simulation physicist uses to simulate the dynamics of rigid bodies. Eg. Impulse Based Dynamics developed by Mirtich
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Deriving the form of radial distribution function in molecular dynamic simulation?

I am trying to derive the equation 8.16 in the attached image from the definition of the radial distribution function. However, I am unable to derive it with proper constants of $\frac{2}{N(N-1)}$ My ...
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QM explanation why hot oil explodes when water pours on it [closed]

I have read this question: Why does hot oil explode when pouring water on it? It explains in a classical way clearly, that the boiling point of oil is hotter then water, and water changes to steam ...
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Understanding simulation output: should the total dipole moment be the sum of its components?

I am trying to understand output from a simulation. I want to calculate a total dipole moment. This is the output I have for an example time step (I assume the three columns correspond to x, y, and ...
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70 views

Why is detailed balance required for thermodynamic consistency?

why does the Wegscheider condition or detailed balance have to be true for chemical reactions and what does it mean to violate it in terms of thermodynamics? here is an attempt to derive a simple ...
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Is quantum energy uncertainty underestimated in liquid molecules?

Liquids have the molecular property that the collision frequency (collisions per time) among the molecules is extremely high; it is at the order of picoseconds. Consequently, the Quantum uncertainty ...
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What is the difference between the differents lennard-jones parameters

I know different lennard jones potentials 12-6, 9-6, 9-3. I think the difference between them is the way they describe long-range interactions,but when I use each of them? Thank you in advance
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How to implement SHAKE algorithm in molecular dynamics for simple systems like linear chain molecule?

3 spherical beads are connected by stiff bond and forms a rod like shape. I am able to perform the Molecular dynamics of them with taking a spring force and a bending force in between them. But for a ...
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Molecular orbital normalization

Suppose that a molecular orbital has the format (not normalized) 0.145A+ 0.844B (1). How do I find a linear combination between A...
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1answer
27 views

Molecular dynamics: metal clusters

I'm working in molecular dynamics with transition metal clusters. The aim is find the melting point, so, it's necessary scale the velocities to increment temperature. I know that I should use ...
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1answer
48 views

When a diatomic ion dissociates, how does the electron density on each atom change?

Let's say, we have a fluorine molecule (F2), and we take 3 electrons from it, so now its bond starts to stretch, and at last the bond breaks and the two atoms are farther and farther away from one ...
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48 views

Nose-Hoover thermostat: real-time average problem?

Many articles as well as the following presentation MD Ensembles and Thermostats, page 23, claim that the principle of the nose-hoover thermostat is "removing the real-time average"-problem. I can ...
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Classical Molecular Dynamics Simulations: Who cares about partition functions?

In most introductory textbooks on molecular dynamics simulations the authors usually tell us how the connection between micro and macro is established using the partition function. Knowing the ...
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Why does a phosphor consist of a tiny amount of 'activator' inside a large host crystal?

Why can't you just smear activator (copper, silver, Europium, etc.) on a surface? Why a large 'host' crystal of (usually) zinc sulfide?
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How to perform the rigid body dynamics using velocity verlet in molecular dynamics?

If instead of a sphere we have few rigid cylindrical rods in a box interacting each other by Lennard Jones potential, which obviously will have the tendency to rotate once hit by other rods. For the ...
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Simulate cluster in a heat bath

I want to simulate a cluster in a heat bath. I always thought I had to simulate it first in the microcanonical ensemble (N,V,E) until I reach the equilibrium. In the equilibrium the temperature will ...
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How to simulate plane Poiseuille flow using Molecular Dynamics? [closed]

I want to simulate 2D plane Poiseuille flow using molecular dynamics (velocity verlet algorithm) but not able to understand exactly to how to do this. Boundary condition is fine, I am confused about ...
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Why are large speaker cones required to to produce loud low frequency sounds?

Is there any reason for why a small speaker cone cannot produce low end sound at a comparable volume to higher frequencies? I can understand how a larger speaker would be in contact with more air and ...
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1answer
44 views

The actual mass of a particle in coarse-grained molecular dynamics

If I use Lennard-Jones unit with the fix langevin command, and set both the mass and damping parameter as 1, does it mean the actual mass of a particle in this ...
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61 views

Basis Functions for Hartree Fock, and Configuration Interaction

I'm about halfway through the book Szabo and Ostlund, and while I think I understand the rough idea of Hartree-Fock and configuration interaction, there is something I would like to clarify. For one, ...
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Probability density of reactions coordinates (collective variables)

I'm reading Chapter 8 of Statistical Mechanics: Theory and Molecular Simulations by M.E. Tuckerman. I have some difficulties understanding one formula (8.6.4). ... If these reaction coordinates are ...
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How accurate is it to use 12-6 LJ potential for interaction between nano-particle and Hydrogen molecule in LAMMPS?

I am trying to simulate a large system containing nano particles (that are fixed in space) and gas molecules passing through the void space between nano particles using LAMMPS. The nano particles have ...
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Stability criterion for leapfrog in relativistic physics

I am doing a 2D MD simulations of charge carriers in graphene using the Leapfrog algorithm. I am trying to prove that, in some specific cases (when distance between particles is small), the method is ...
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1answer
64 views

How is atomic position expressed in QM?

I am trying to understand how DFT works. I understand how to express the position of an atom or molecule in terms of the positions of the nuclei and electrons by setting up a Hamiltonian expressed in ...
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83 views

Can Einstein relation be used to calculate mobility under equilibrium dynamics?

In weak field non-equilibrium dynamics, mobility can be calculated by Einstein relation $\mu=\frac{eD}{K_BT}$, where $D$ is diffusion constant. Mobility can also be calculated by the definition $\mu=...
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81 views

Screening of a coulomb-like potential

Imagine that we have a potential in the form of: $U(r) \propto \frac{1}{r^n}$ in a 2D system, with the high concentration of particles interacting with the above potential. How do you find the ...
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What would happen to a liquid's pressure if interaction between molecules ceased to exist?

If a gas is composed of molecules who attract eachother, then its pressure would increase were the interactions to suddenly disappear. This can be quantitatively and qualitatively discussed using Van ...
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142 views

Series expansion of $N$-particle potential energy

I am trying to understand the so-called Taylor expansion (or series expansion) of potential energy of a system of $N$-particles. This expanded form is stated without derivation in some molecular ...
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478 views

Where do the Lennard-Jones dimensionless/reduced units come from?

I'm a little bit confused as to where the expressions for the Lennard-Jones Potential Dimensionless units shown in this Wikipedia chart come from. I know they're derived from the L-J force equation ...
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102 views

Multiparticle simulation and Velocity Verlet Algorithm

The Velocity Verlet algorithm requires using an updated particle acceleration to compute and updated velocity. If that acceleration depends on a force that depends on distance to the other particles, ...
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Looking For a Relativistic Probability Distribution for Rotational Velocities of polyatomic molecules

I've been trying to find a suitable probability distribution function for the rotational velocity of molecules around T = 300K. It doesn't need to be incorporate QM effects, though I don't mind if it ...
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What is the difference between density functional theory and ab initio molecular dynamics?

I feel like I should know the answer to this question. But in standard implementations of (say) plane-wave DFT in softwares like VASP, the atomic positions are moved based on the Hellman-Feynman ...
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What are phonon frequencies in solids? How are they related to the interaction potentials between the constituent atoms?

I was reading a paper on self-assembly of colloidal structures, where it was mentioned that only solids with real phonon frequencies are mechanically stable. And the authors go on to manipulate the ...
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Venturi effect on molecular level

Is there a good explanation why the pressure becomes lower on the narrow part of the venturi pipe? I'm not interested in the newton explanation or pressure differences explanation. I want to ...
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1answer
89 views

Why does using deuterium mass for hydrogen improve convergence of molecular dynamics simulations of water?

I've come across many papers performing ab initio MD (Carr-Parinello or Born-Oppenheimmer) simulations of water that use the deuterium mass for hydrogen. And they state that this helps improve ...
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71 views

How do we take temperature into account in Ab-initio molecular dynamics simulation?

In Ab-initio molecular dynamics simulations, we use Ab-initio methods for calculating the ground state electronic energies of the atomic configurations visited along the dynamics. The atomic forces ...
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What type of potential is suitable for ion bombardment in Molecular Dynamics?

I would like to study ion bombardment on targets with molecular dynamics, especially on oxides. So far I ran conclusive tests with Lennard-Jones potentials, but I would like to obtain better ...
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Keeping the electronic configuration in the ground state is expensive in Ab-initio MD?

In E. Sandré & A. Pasturel's An Introduction to Ab-Initio Molecular Dynamics Schemes If using small time steps (typically in the order of a few tenth of femto-second), the changes in the ...