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
0answers
13 views
How does the potential energy surface of a molecule look like?
How do you find the PES(Potential Energy Surface) of molecules, and why are they interesting? Can you please direct me to some source regarding the same? How does the energy landscape of the molecule ...
0
votes
0answers
16 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 ...
0
votes
0answers
26 views
From cartesian to internal coordinates for the classical molecular vibrational problem [on hold]
If we suppose to have a generic molecule made by $N$ nuclei, describing them with cartesian coordinates, the Lagrangian of this system, using an harmonic approximation for the potential energy is:
$$L=...
2
votes
1answer
40 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
21 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
27 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
17 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
28 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
22 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
30 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,...
4
votes
2answers
260 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
64 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
49 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
58 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
13 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
99 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 ...
0
votes
0answers
24 views
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 ...
3
votes
1answer
71 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
9 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
103 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 ...
1
vote
1answer
131 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
55 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
62 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
37 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
65 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
99 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
67 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
41 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
100 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 ...
0
votes
0answers
29 views
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 ...
7
votes
1answer
131 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
73 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
100 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
348 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 ...
1
vote
2answers
62 views
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,...
0
votes
1answer
50 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 ...
3
votes
1answer
254 views
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 ...
4
votes
0answers
110 views
Why is it a disadvantage for Langevin dynamics to be non-reversible?
In Molecular Dynamics, it is commun to use a Langevin thermostat to maintain a constant temperature. However, it is often written that the Langevin Thermostat not being time reversible is a ...
2
votes
1answer
45 views
Generalizing the “Extended System Method”
After looking into molecular dynamics simulations for NVT and NPH ensembles, I noticed a peculiar kind of Lagrangian transform they do.
Starting with a Lagrangian like,
\begin{align}
\mathcal{L}(q, \...
1
vote
0answers
61 views
TINKER molecular modeling software package- Boltzmann constant units [closed]
I use the TINKER molecular modeling software package (version 7.1.2) for computational physical chemistry. There is an extra file (extra1.f) included for the user to edit and incorporate in their own ...
0
votes
1answer
133 views
How do the molecules form a solid object?
It's known that every molecule is moving around at any time. But how can they form a solid object, like a cup, or a human? Also, I think according to statistics, all molecules should have been ...
1
vote
1answer
73 views
Oil-water interface simulation using Gromacs
I would like to perform a decane/water(tip4p) interface simulation using GROMACS to analyse the fluctuation of the interface over a long period of time (50ps - 1ns).
Though I have a rough idea on ...
0
votes
2answers
99 views
Thermostat code for molecular dynamics with angle dependent potential
I'm building molecular dynamics code for the specific purpose of simulating Janus particle because no package supports the custom angle dependent potential to my knowledge.
I'm building thermostat ...
7
votes
1answer
349 views
Molecular Dynamics Software for Coarse Grained Polymers
I am looking around for MD software that I can use to simulating polymers and I can't decide which software I should use.
I would like to simulate the swelling of crosslinked polymers, and I would ...
1
vote
1answer
135 views
How can I detect a phase-transition in a molecular dynamics simulation?
I am doing a molecular dynamics simulation with FCC metals bulks in the NVT ensemble. I have to detect or study the phase-transition from solid to liquid
when heating the bulk. I use a Nose-Hoover ...
