Questions tagged [molecular-dynamics]
Molecular dynamics (MD) is an approach used for simulating dynamic processes through successive integration of Newton's equations of motion.
298
questions
31
votes
3
answers
4k
views
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 ...
- 421
0
votes
3
answers
44
views
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 ...
- 146
0
votes
2
answers
75
views
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 ...
- 346
0
votes
0
answers
9
views
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 ...
- 11
2
votes
1
answer
45
views
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 ...
- 1,572
0
votes
0
answers
12
views
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 \...
- 1
0
votes
0
answers
47
views
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 ...
0
votes
0
answers
30
views
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-...
- 36
0
votes
0
answers
41
views
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 ...
- 1
0
votes
0
answers
15
views
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 ...
- 557
0
votes
0
answers
12
views
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 ...
- 123
0
votes
1
answer
19
views
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 ...
- 197
0
votes
0
answers
17
views
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 ...
0
votes
0
answers
20
views
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 ...
- 139
1
vote
1
answer
57
views
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 $\...
- 113
1
vote
2
answers
47
views
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&...
- 49
6
votes
2
answers
231
views
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}...
- 432
0
votes
0
answers
94
views
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 ...
0
votes
0
answers
24
views
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 ...
0
votes
0
answers
31
views
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 ...
- 869
0
votes
0
answers
21
views
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 ...
- 197
1
vote
2
answers
56
views
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}) $
...
- 113
1
vote
1
answer
39
views
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 ...
- 11
0
votes
1
answer
24
views
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 ...
- 167
1
vote
1
answer
46
views
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 ...
- 329
1
vote
0
answers
46
views
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 ...
- 63
1
vote
0
answers
12
views
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 ...
- 350
0
votes
1
answer
33
views
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 ...
- 13
0
votes
2
answers
75
views
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 ...
14
votes
3
answers
4k
views
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 ...
- 373
1
vote
1
answer
84
views
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}')}[...
- 21
0
votes
1
answer
29
views
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, ...
1
vote
0
answers
46
views
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 ...
- 553
0
votes
0
answers
19
views
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 ...
- 689
0
votes
0
answers
6
views
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 ...
- 553
0
votes
0
answers
28
views
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 ...
- 101
3
votes
2
answers
156
views
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 ...
4
votes
3
answers
296
views
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 ...
- 842
37
votes
7
answers
5k
views
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 ...
- 527
1
vote
0
answers
21
views
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, ...
- 351
0
votes
2
answers
81
views
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 ...
- 13
0
votes
1
answer
246
views
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 (...
- 2,467
0
votes
1
answer
30
views
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 ...
1
vote
2
answers
81
views
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]$$ as ...
- 557
1
vote
0
answers
33
views
Conditions on freezing water
Observing the freezing phenomenon of river, here are some questions pop up.
Comparing with pure water, impurity in water will alter melting point, what are the qualitative and quantitative explanation,...
- 455
2
votes
2
answers
63
views
When is molecular chaos dynamical chaos?
It is very common to have uncorrelated velocities in chaotic dynamical systems. Yet, we should be wary in equating the two quite different meanings of chaos.
Instead of matching dynamical chaos to ...
- 203
1
vote
0
answers
74
views
Pressure tensor in brownian dynamics
I need to calculate the pressure autocorrelation function in a Brownian dynamics particle simulation to get the viscosity (which is proportional to the time integral of this function):
$$ \left \...
- 11
0
votes
0
answers
17
views
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 ...
- 335
0
votes
0
answers
40
views
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 ...
- 557
0
votes
2
answers
121
views
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 ...
- 886