Questions tagged [molecular-dynamics]
Molecular dynamics (MD) is an approach used for simulating dynamic processes through successive integration of Newton's equations of motion.
0
votes
1answer
17 views
How to simulate plane Poiseuille flow using Molecular Dynamics?
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 ...
5
votes
3answers
105 views
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 ...
1
vote
1answer
33 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 ...
0
votes
1answer
24 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, ...
1
vote
0answers
20 views
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 ...
0
votes
0answers
26 views
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 ...
2
votes
0answers
31 views
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 ...
1
vote
1answer
60 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 ...
0
votes
1answer
54 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=...
0
votes
1answer
56 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 ...
0
votes
1answer
37 views
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 ...
1
vote
2answers
97 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 ...
-1
votes
2answers
153 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 ...
1
vote
2answers
50 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, ...
1
vote
0answers
23 views
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 ...
0
votes
0answers
44 views
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 ...
2
votes
1answer
49 views
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 ...
0
votes
0answers
38 views
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 ...
1
vote
1answer
42 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 ...
0
votes
1answer
31 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 ...
1
vote
0answers
32 views
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 ...
0
votes
1answer
25 views
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 ...
0
votes
0answers
11 views
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 ...
1
vote
1answer
39 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,...
5
votes
2answers
291 views
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 ...
1
vote
1answer
100 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 ...
1
vote
0answers
50 views
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 ...
0
votes
1answer
91 views
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 ...
0
votes
0answers
14 views
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 ?
0
votes
1answer
191 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 ...
3
votes
1answer
99 views
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 ...
1
vote
0answers
37 views
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, ...
0
votes
0answers
12 views
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 ...
0
votes
1answer
157 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 ...
2
votes
1answer
289 views
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'...
0
votes
1answer
66 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 ...
0
votes
0answers
84 views
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 ...
0
votes
0answers
41 views
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 ...
1
vote
0answers
41 views
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 ...
0
votes
1answer
128 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 ...
1
vote
0answers
112 views
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 ...
1
vote
1answer
83 views
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 ...
0
votes
1answer
47 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.
0
votes
1answer
145 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 ...
1
vote
0answers
40 views
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 ...
7
votes
1answer
152 views
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 ...
1
vote
2answers
76 views
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 ...
0
votes
1answer
139 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.
...
1
vote
0answers
22 views
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 ...
1
vote
1answer
540 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 ...
