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 aren't Runge-Kutta methods used for molecular dynamics simulations?

One of the most used schemes for solving ordinary differential equations numerically is the fourth-order Runge-Kutta method. Why isn't it used to integrate the equation of motion of particles in ...
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What forces act on an element taken in a body which is subjected to no external forces?

Consider a block (rigid) which is lying on a table. If we take a differential element in the block and try to draw its Free-body diagram, will there be any forces other than gravitational force acting ...
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Why do two molecules of an element attract each other?

I was thinking about molecular attraction and a question suddenly struck in my mind which is 'Why do two molecule of an element attract each other?' The answer is easy when we discuss about compound ...
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Decrease in average kinetic energy at Lennard-Jones phase transition

I have written a molecular dynamics simulation to model argon using the Lennard-Jones potential. I am investigating the behaviour of the system near it's melting point for a specific pressure and ...
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How does the wringing of gauge blocks make them stick together?

I was surprised to learn about gauge blocks and how you stick them together. The blocks have very smooth surfaces and still they stick by wringing ( https://youtu.be/2lOOl3VxOtE ). One speaks of ...
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Nearest Neighbor Entropy Estimate Differentiation

I am interested in differentiating an effective potential based on the following nearest neighbor estimate from [1]. $$H_n = \frac{1}{n}\sum_{i=1}^n \ln(n\rho_{n,i})$$ where, $$\rho_{n,i} = min_{j \...
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Schrodinger operator with matrix potential and Green's function

Clearly Schrodinger operators with matrix potentials appear very naturally in molecular dynamics/quantum chemistry, particularly when considering a crude adiabatic basis or diabatic basis for an ...
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Rate Dispersion is the distribution of rates on a rate spectrum. What are the quantities physically associated in a Rate Spectrum?

I am working on a project to decipher the "origin of rate dispersion" arriving because of Heterogeneity in our system using correlation function analysis in Python. Rate Dispersion, non-...
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Uniform radial distribution function

I am attempting to properly account for excluded volume effects on the radial distribution function for a fluid. A correction for these effects has been proposed back in 2000 in this paper by Hartnig ...
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Unable to recreate plot for anisotropic Gay-Berne potentials from paper

I am trying to make a plot of the Gay-Berne potential using Mathematica. I am following this paper and I am trying to recreate Fig. 2. This is figure 2: To save time, the equations from the paper are ...
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Molecular Dynamics to study crystallographic phase transition

I want to study the crystallographic phase transitions of crystals with increasing temperature. Which freely available MD package should I choose.. which has easily available tutorials/example input ...
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Displacement distribution Molecular Dynamics

I have a file "traj.dat" with the trajectory of $N$ particles for $M$ frames separated by $\Delta M$ steps (with a time-step $\Delta t$). I often compute Mean Square Displacement (MSD) of ...
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What is the reason that in DPD (LAMMPS) we can define a protein (or any material with a flexible geometry) without the material loosing its shape?

I am new to LAMMPS/DPD (Dissipative particle dynamics), but as I read through DPD model which is a coarse graining model, there are only three main forces between beads (beads are the spheres ...
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LAMMPS: How to enter a simple potential for Dissipative Particle Dynamics (DPD)?

I apologize if this is off-topic and if so would be grateful for someone to point me to a relevant source of information. Dissipative Particle Dynamics (DPD) is a quick simulation technique that ...
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Hamiltonian Monte Carlo: Kinetic and Potential energies

In HMC (good intro here) the Hamiltonian is defined as \begin{align} H(p,\theta) &= -\log p(q,\theta) \\ &= -\log p(q) - \log p(\theta). \end{align} Here $p$ is the momentum coordinate and $\...
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Question about molecules and their movement

This question might be nonsensical and, if it is, please leave a reply so I know and can remove it. I'm currently learning about basic thermodynamics and was thinking, if there is some "average&...
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Vibrational spectrum of diatomic molecule from Schrödinger's equation

I'd like to find the vibrational spectrum of a diatomic molecule from its potential, which can be approximated as $$V(R) = -V_0\Big[ \frac{1}{4}\Big(\frac{R_0}{R}\Big)^4 - \frac{1}{8}\Big(\frac{R_0}{R}...
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Translation of reduced units to real units for Lennard-Jones system and the Law of Corresponding States

I am struggling to completely make sense of a few sentences I came across in Frenkel and Smit (pg. 41): One may wonder why it is convenient to introduce reduced units. The most important reason is ...
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Can Lennard-Jones parameters (epsilon) be zero?

I was told that very often, intermolecular potential parameters (e.g. Lennard-Jones or Moorse etc.) are determined empirically via manual adjustment to reproduce experimental properties such as ...
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Can the lifetime of a broken covalent bond be calculated?

According to a paper (molecular dynamic simulation) published in 2018,(https://www.scirp.org/journal/paperinformation.aspx?paperid=83351) the Maxwell-Boltzman distribution is also valid for the number ...
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Structural Factor and Intermediate Scattering function

I'm working with Molecular Dynamics simulations. I have computed the radial distribution function $g(r)$ for a pseudo-2D system (the particles are not disk, they have volume, but z-coordinate is much ...
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2 answers
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Confusion on molecular dynamics (MD) simulation units leading to absurd acceleration values

I am trying to code up a very simple MD simulation in order to learn more about it. I am using the Leonard-Jones potential, expressed as $ V=4\epsilon (\frac{\sigma}{r}^{12}-\frac{\sigma}{r}^{6}) $ ...
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Partition Function from Dispersion Relation in Molecular Dynamics

I’ve seen there are ways to compute the dispersion relation of a crystal from molecular dynamics. An example of how to do this is discussed in this question: Computing phonon dispersion from molecular ...
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Modes of Motion of A Lennard-Jones Cluster

I am trying to analyse the dynamics of a cluster of 79 atoms. The context of the question is that each atom in the cluster (which has Lennard-Jones interactions between the atoms) is displaced by a ...
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What does the Combined Notation $\left<\text{abc}\right>\{\text{def}\}$ mean in Crystallography?

I have come across some notation of the form $\left<\text{abc}\right>\{\text{def}\}$ in a paper on the Solid-Liquid Coexistence Molecular Dynamics simulation of single element materials, please ...
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Thermal Conductivity of a Harmonic Lattice

I have been trying to compute the conductivity using the Green-Kubo formula obtained from molecular dynamics simulations. I used a square lattice and a harmonic potential and I consistently get a ...
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Intuition behind residence times measurement through NMR

I have read that residence times of molecules near to other molecules can be obtained trough NMR experiments. For example, the average time that a average water molecule stay close to a protein. In ...
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Which are the temperature limits that models as spc or spc/e describe better water in Molecular Dynamics Simulations?

I would like to simulate an organic molecule in water using spc or spc / e models and carry out an annealing. I think that a good parameter to define the temperature limits is to take into account how ...
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Why energy expectation values (Energy) are functions of coefficients of corresponding trial wave functions in variational principle?

The method consists of choosing a "trial wavefunction" depending on one or more parameters and finding the values of these parameters for which the expectation value of the energy is the ...
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14 votes
3 answers
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When two molecules collide, does it produce a sound?

When we are in an empty room with no one around, we don't hear any sound, but there are billions of atoms and molecules that are colliding at the same instant. So my question is, when two molecules ...
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Problem with particle correlation functions

Given a probability density $\rho(\textbf{r})$ defined in a volume $V$ in $2$ or $3$ dimensions one can define the autocorrelation function as: $$ \Phi(r) = \frac{1}{4 \pi}\int_{V}{\rho{(\textbf{r}')}[...
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Recovering data from LAMMPS MD simulation

I'm simulating a Lenard Jones fluid with LAMMPS. I already have the simulation but I have the problem of recovering data. I'm interested in pressure vs time, pressure vs position, temperature vs time, ...
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Angular momentum in molecules

When using the Born-Oppenheimer approximation to find the electronic energy levels of a diatomic molecule, $L^2$ doesn't commute with the Hamiltonian i.e. $l$ is not a good quantum number, but its ...
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How to use Bennett Acceptance Ratio (BAR) method to calculate chemical potential?

In Understanding the Bennett Acceptance Ratio (BAR) method the BAR method is explained. I do not understand how to use it to compute chemical potential (I don't know what $U_0$ or $U_1$ is). I think ...
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Isotope shift effects in molecules

There are some papers that present the dependence of energy levels on the nuclear mass for a diatomic molecule and a general formula for the case of closed shell molecule was given in some papers by ...
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Looking for input to a simple transformative Ab initio molecular dynamics (AIMD) trajectory simulation

I'm looking for a simple Ab initio molecular dynamics (AIMD) simulation of some small molecular system that I can run myself on a desktop computer. I want a molecular system that actually changes ...
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2 answers
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Why is the heat energy used to overcome the intermolecular force only when it reaches melting point or boiling point?

When heat is supplied to water, for example, the temperature of water increases with the rise in heat energy but when the temperature reaches $0^\circ$centigrade or $100^\circ$centigrade, the heat ...
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4 votes
3 answers
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Why do molecules behave classically at high temperatures?

In chapter 6 of "Charge and Energy Transfer Dynamics in Molecular Systems", the authors consider diatomic molecules in contact with a heat bath. We have established before that the nuclear ...
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7 answers
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When I put my hand on a hot solid why don't the particles transfering heat to my hand exert a force on it?

When I put my hand on a hot metal (say) solid, I can feel my hand heating up. I suspect this is caused mostly by particles (electrons, atoms, ...?) from the solid colliding with the particles that ...
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Effects of electroplating soft magnetic materials

Considering how electroplating adheres molecules and compounds on a molecular basis, how would electroplating a soft magnetic material, such as an electromagnet, with diamagnetic atoms, like bismuth, ...
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Algorithm for Grand Canonical Monte Carlo (GCMC) Molecular Simulation - Initialization

I am trying to make sense of the GCMC algorithm in Frenkel and Smit. I do not understand the conditional statement if a particle is to be displaced or exchanged(removed or added) in a Monte Carlo ...
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Energy conservation in systems with discrete time

Numerical simulations of classical particle dynamics usually break energy conservation due to discretization of time. Is there any explicit numerical scheme that does not break energy conservation (...
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How to specify the dimension of the simulation box to run molecular dynamics simulation

I want to study the physical properties of binary liquids, molecular dynamics simulation using gromacs software is used to simulate the liquids. To set the initial coordinate configuration, how do we ...
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1 vote
2 answers
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Proof of pressure of system in molecular dynamics

I am studying barostatting algorithms, and I am seeing this equation quite a bit: $$ PV = \frac{1}{3}\left[ \sum _i \left( \sum _{i<j} F_{ij} \cdot r_{ij} \right)+ \frac{|p_i|^2}{m_i}\right]$$ as ...
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Conditions on freezing water

Observing the freezing phenomenon of river, here are some questions pop up. Comparing with pure water, impurity in water will alter melting point, what are the qualitative and quantitative explanation,...
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2 answers
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When is molecular chaos dynamical chaos?

It is very common to have uncorrelated velocities in chaotic dynamical systems. Yet, we should be wary in equating the two quite different meanings of chaos. Instead of matching dynamical chaos to ...
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Pressure tensor in brownian dynamics

I need to calculate the pressure autocorrelation function in a Brownian dynamics particle simulation to get the viscosity (which is proportional to the time integral of this function): $$ \left \...
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Does viscosity arise from the increase in intertia created by the movement of molecules?

Cohesion is how strongly a substance holds itself together, and viscosity has been described as the substance's internal friction. Viscosity has mostly been explained to me via allusions to substances ...
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Why is Ewald summation faster than normal summation?

I posted this on the Mathematics SE, but wasn't sure if it was purely a mathematical problem. If I should take this down because of cross-posting rules, I will do so gladly. I have been trying to ...
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Why does introducing more variational parameters improve the accuracy of our approximation

If we consider the variational method in quantum mechanics as outlined in this wikipedia article: https://en.wikipedia.org/wiki/Variational_method_(quantum_mechanics) It is stated that 'Some choices ...
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