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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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 ...
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Photoreactivity/photofragmentation dependence on pressure

Most of the photofragmentation studies I see are done in vacuum or lower pressure. Is this just because of the experimental limitations or the photofragmentation doesn't matter the surrounding ...
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Energy differentiation with cut-off function

I am a new learner of molecular dynamics (MD) simulations methods and has a simple question regarding handling of cutoff functions. In MD, pairwise energy between two atoms is assumed to be a function,...
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How can I include variable particle number in a Brownian dynamics simulation?

I programmed a Brownian dynamics simulation in two dimensions. (Coarse-grained proteins on surfaces with interaction potentials i.e. patchy particles.) Now I want to allow particles to leave or enter ...
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Linear momentum conservation for interaction between rigid body and point mass

Let's say I have an interaction potential between a rigid body and a point mass expressed in spherical coordinate : $V=V(r,\theta, \phi)$. The coordinates $r, \theta$ and $\phi$ specify the position ...
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In Monte Carlo integration for Molecular dynamics simulation, why is a Boltzmann distribution assumed?

In statistical physics, The calculation of partition function for an ensemble takes a Boltzmann's distribution of the Hamiltonian. Similarly, In Monte-Carlo integration of Molecular Dynamics ...
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Body Rotation in a Molecular Dynamics Simulation

I have been trying to simulate particles trapped in a parabolic potential in two dimensions. Due to the circular symmetry of the system, in the ground state at zero temperature, the particles are seen ...
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Coordinates of all the atoms in protein molecule for the given Ramachandran angles for all the peptides

How to determine coordinates of all the atoms when ramachandran angles are given ? Can someone suggest some references to determine all the coordinates for the given Ramachandran angles ?
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Specific heat capacity at constant pressure formula

I want to calculate specific heat capacity at constant pressure for a single walled carbon nanotube by using of fluctuation in enthalpy. The fluctuations were obtained from molecular dynamics ...
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What is water pressure, really? [duplicate]

It's easy for me to imagine gas pressure on a molecular level. More pressure means that more molecule bounce against the thing you are measuring, or the molecules hit it with more speed or the ...
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Generalized reaction rate for elementary process

Most textbooks give the reaction rate $$r = k [\mathrm{R}_1]^{a_1}[\mathrm{R}_2]^{a_2} \tag{1}$$ for the elementary process $a_1 \mathrm{R}_1 + a_2 \mathrm{R}_2 \rightarrow \mathrm{P}$. However, ...
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When do gas molecules deviate from Maxwell Boltzmann distribution?

The velocity of the gas molecules at room temperature obey Maxwell Boltzmann distribution. When we say velocity, the distribution is true for each component right ? means vx, vy and vz are in MB ...
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Normal modes: how to get reduced masses from displacement vectors, atomic masses and vibrational frequencies

I'm calculating normal vibrational modes in a large molecular system. My goal is to obtain, for each normal mode, the vibrational frequency, the list of displacement vectors and the reduced mass. I'...
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Pair correlation function vs Bond length distribution of a van der Waal dimer

For a weakly bonded molecular dimer (when two atoms are interacting through van der Waal (vdW) interaction). Do the distribution of pair correlation function and vibrationally average bond-length ...
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Quantifying physical intuition about heat and motion

Assume that we are in deep space. There are two objects Orange and Blue. Initially, Orange is at a temperature of 200K and Blue is at 1000K. Consider the following scenarios. For now assume that there ...
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What is the narrowest possible functioning straw that could be made?

Let's assume that the straw/pipe/tube can be made of any material, but it should be at least 100 times as long as the inside is wide. How narrow could the inside of the straw be made before it is no ...
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How to get the phase transition diagram for a coexistence phase simulation?

I am running a lammps program to get the phase transition diagram. one for gold and the other for silicon. I am measuring the melting point by investigating the growth of each phase at different ...