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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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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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Some clarifications about Point Groups rapresentations for molecules

This is what I've understood until now about this subject, please confirm if what I write is true or not. Choosen one molecule, there is a certain number of symmetry operations which this molecule ...
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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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35 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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31 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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22 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 ...
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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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34 views

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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88 views

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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142 views

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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Determining the sign (+/-) of the total work done on separating two molecules along a certain distance - AMBER16

I am currently moving two sugar molecules apart and would like to analyse the work done on separating them (and thus moving them apart from a distance of 3.5 Å to 30 Å). The values I am given by this ...
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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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Simulating only small parts of macromolecules

I've recently gotten into molecular dynamics (MD), and I was wondering the following: how can one simulate only small parts of proteins, e.g. up to 10AA? I am fond of e.g., Gromacs, where whole ...
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131 views

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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60 views

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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time autocorrelation function code for energy trajectory over time

I would like to calculate the time auto correlation function of the energy in time trajectory of a molecular dynamics simulation by hand. I have an Nx1 array of energies over N timesteps to show the ...
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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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91 views

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 ...
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Difference between dynamics of system evolving by Langevin equation with and without inertia

Each component of a many-particle system can be described by a Langevin equation: $$m_i \frac{d^2r_i}{dt^2} = F_{config} + \gamma \frac{dr_i}{dt} + F_{noise}$$ Where $F_{config}$ depends on the ...
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magnetic and electric interactions in atomic level

From what I understand Van der Waals (VDW) forces are the primary source of inter-molecular interaction. There are three different possible origins for van der Waals forces: permanent dipole-permanent ...
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45 views

Time step of MD simulation

I am a beginner in MD simulation, my question is what occurs if instead of 0.5 femto-second I choose 5 ft as time step of my simulation I am doing MD with protein.
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114 views

Structure factor calculation for non-cubic lattices

I have an equilibrated trajectory from a molecular dynamics simulation and I would like to calculate the structure factor using the atomic positions. I think I am able to do it right for cubic ...
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Is there any method to calculate surface tension of packing of particles under external potential

I want to calculate surface tension of stacking of particle which the surface is under a repulsive potential. The repulsive potential applying the force to the particles to have a surface (or ...
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Fitting of force constants from vibrational frequency

From my understanding, the force constants in a molecule, for example methane, can be fitted using vibrational frequency data from experiment by diagonalising the hessian etc. My confusion lies in ...
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What happens if a metal wire that was one-atom in thickness was pulled across a finger?

What would happen if a metal wire that was one-atom was pulled across your finger? Would it cut off your finger, or would it pass through your finger without harming you? What if the metal one atom ...
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Software for simulating gas of hard particles (i.e. polyhedra?)

I was wondering if there existed a kind of software I could use to simulate a gas of polyhedra, such as tetrahedra. They would interact through entropic interactions only, i.e. excluded volume. I'm ...
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114 views

How to simulate a phase transition in Molecular Dynamics?

I am trying to simulate the phase transition for gold and silicon separately using LAMMPS. I got the melting point for gold right using the below code. ...
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How to classify archimedean solid quasicrystal made by stacking spheres

I have two sphere packing structures (i.e. 3N-coordinates of each structure). One is rhombicosidodecahedron and the other one is truncated icosahedron. They are clearly distinguished when they are ...
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437 views

Maxwell Boltzmann Distribution in Molecular Dynamics Simulation

I have an MD simulation that I'm pretty confident it works correctly. One of my tests was to check if the velocity distribution follows a Maxwell Boltzmann distribution. I printed out the velocity ...
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Physics law in this statement, if there are any

happened to find an interesting line and would like to know if there is any law in physics which confirms even partially that and, if so, which is/are these laws (so that I can look up for them myself,...
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52 views

Minimum image convention and the atom “seeing” itself

The minimum image convention in molecular dynamics can be state as: A particle in the central square must not interact with one of its neighbors in the central square and an image of this neighbor in ...
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Computing Entropy properly during Molecular Dynamics simulation

When simulating simple system to test out Stat Mech (ie. non-coupled), I was able to compute entropy by binning the particles and using the Shannon entropy formula. For more complex systems, I ...