Questions tagged [intermolecular-forces]
Refers to forces that mediate interaction between molecules, including forces of attraction or repulsion which act between molecules and other types of neighboring particles, e.g. atoms or ions.
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DFPT vs analytical nuclear gradient
I have read some literatures about the gradient wrt. atom positions of the DFT energy, and find different methods one commonly used in MD(analytical nuclear gradient,pulay's paper), and another ...
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How to check the units from ASE get_forces() function?
Here is a little python code that loops through a molecular dynamics trajectory (performed with the ASE package) and outputs the forces on the atoms at each frame:
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Is it okay to use semi-empirical methods to optimize structures if I perform high-level energy calculations?
For non-covalent systems comprised of small-molecule monomers, folks are usually interested in understanding the interaction and binding energies of small (gas-phase) clusters ... things like $\ce{X(...
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Energy balance in a molecular dynamics simulation with ghost atoms and periodic boundary conditions?
I am performing a simulation in LAMMPS with granules (DEM) and I had a question regarding the conservation of energy. If an interaction happens where one granule is in the simulation box and the other ...
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Is it possible to evaluate rotational and vibrational partition functions for diffusion in the Eyring Theory of Absolute Rates?
Let us consider the usual expression for Diffusion processes and diffusion coefficients in the Eyring's theory:
$$D=\lambda^2k = \lambda^2 \frac{k_BT}{h}\frac{\Omega_\ddagger}{\Omega}e^{-\frac{\...
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Rotational invariance of anisotropic polarization models
After writing out this question, I actually figured out the answer, but I am surprised I haven't seen this detail mentioned in almost any paper on the topic, so I will answer my own question here in ...
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Developing a machine-learned interatomic potential for molecular dynamics
There are few questions in this SE about the advantages/disadvantages of machine-learned interatomic potentials in molecular dynamics, but there is not much discussion on how to make them. I thought ...
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Which equation makes it possible to calculate the forces of attraction between a surface and molecules?
Which equation makes it possible to calculate the forces of attraction between a surface and molecules? Is there any free software that implements such a calculation?
[Clarification 1] Between a ...
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What's a quick way to get a molecular bond length using a Newtonian model?
Can anyone spare me a clue on this?
I'm a self-taught student of Molecular Geometry trying to learn more about methods in modeling. After some extensive reading and study, it felt like it should be ...
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Periodic boundary conditions or spherical potential? [closed]
I was wondering whether you know if there is any sort of literature discussing whether periodic boundary conditions or spherical potentials could be better or worse for QM/MM or MM simulations, their ...
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Sigma Profile in COSMO - RS model [closed]
As far as I understand, sigma profile in COSMO - RS is a probability distribution of screening charge density for certain molecular surface segment.
In COSMO - RS, molecular surface area is segmented ...
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Gromacs generate forces using .pdb topol.top and .mdp file [closed]
Given the start configuration (.pdb), topology file (topol.top) and run file(water.mdp).
I want to generate the forces on atoms. I tried, using:
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What does the shape of the radial distribution function(RDF) indicate? [closed]
From my understanding, generally in the RDF plot for liquids, the value of $g(r)$ goes to a maximum near the first solvation shell and then goes to a minimum and then slowly tapers off to the value of ...
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How might inclusion of a Grimme dispersion correction influence a simulation of a dense liquid that is not water?
I adapted an example first-principles water simulation to do simulations of liquid SiO2, but did not know what I was doing and did not remove a Grimme dispersion correction term.
It would be great to ...
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How do you incorporate hydrogen bonding into molecular simulations?
How do computer simulations of liquid hydrogen-bonding systems incorporate hydrogen bonding? Since I think hydrogen bonding has mixed covalent and electrostatic character, wouldn't you need something ...
user2026
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What is the polarization catastrophe?
I heard about the polarization catastrophe in a talk about polarizable force fields.
The speaker talked about how the dipole induction is damped at short range to avoid the “polarization catastrophe&...
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Should I use a different cut-off scheme for non-bonded interactions when simulating a system with MD in vacuum?
I am currently doing a simulation of the behaviour of various sizes of water droplets (~100-1000 water molecules) in vacuum. I am using NAMD with the spherical boundary conditions to keep the droplet ...
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Molecular dynamics to reproduce dispersion interactions [closed]
I'm trying to simulate the behavior of chromophore molecules incorporated into a polymer under an external electric field.
I've tried to use classical molecular dynamics (GROMACS) but it's unable to ...
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References for Electrostatics Calculations Used in Molecular Dynamics
I'm looking for classic references that describe the usual electrostatic contributions which have to be calculated in molecular dynamics simulations. I find it very hard to apprehend what different ...
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Are there good tutorials that explain how to use experimental data to customise the force field in AMDock Vina?
I am not a chemist, but I know how to use AMDock to predict the binding affinity of a small molecule to a protein.
There is a particular target for which AMDock Vina, with its default force fields, ...
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Can the NCI (noncovalent interaction) index be generated starting with psi4?
Can NCI[1] index plots be generated starting from psi4? I'd be happy to just generate the NCI index values and mesh the isosurface myself.
With a long-term goal to visualise various medicinal-...
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Should I add vdW interaction to estimate chemical potential of metallic elements?
I am considering layered oxides $\ce{LiCoO2}$. Previous papers suggested that vdW interaction should be added to get lattice parameters closer to experimental data. I would like to dope other elements ...
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Empirically determining thermostat damping factor
Is there a way to empirically determine an appropriate thermostat damping factor given a timestep size and a numerical integration method? For example, I would like one for the surface and the ...
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How does one compute the boiling point of a liquid made of a particular molecule?
This question is in relation to Anomalous boiling point of "iso-" alkanes on Chemistry SE.
I want to compute the boiling point of the different isomers of an n-carbon alkane to check what ...
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Rule-of-thumb for Morse potential cutoff in molecular dynamics?
Is there a rule-of-thumb for selecting a cutoff for the Morse potential in molecular dynamics simulation? For instance, is it typically some multiple of the equilibrium distance?
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Simulating breaking bonds in molecular dynamics
How does one introduce the possibility of breaking a bond in a molecule during MD simulation?
I only found the cases when we just introduce the harmonic potential $U_{ij} = \frac{1}{2}k(r_i - r_j)^2$ ...
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DFT modeling intermolecular interactions
Density Functional Theory based codes evaluate quite successfully intramolecular forces responsible of the atomic bonding. Within this technique one is able to obtain molecular relaxed structures that ...
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Benchmarking data for Ewald summation algorithms
Are there good benchmarks available for testing homemade Ewald summation code?
Optimally it would be very nice if there was several types of systems.
NIST has a very nice benchmark for energies of ...
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What is the appropriate way of determining a value for the Hubbard-like potential U for LDA+U / GGA+U calculations?
It is known that neither LDA or GGA correctly account for the strong on-site Coulomb interaction of localized electrons[1]. A cost-effective way of correcting this is by using a Hubbard-like term $U$. ...
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What are the different ways of calculating dispersion constants?
There are many different dispersion corrections out there. The most famous is D3 [1] (and the new D4 [2]), but there's probably other approaches too. The dispersion energy can be written as:
$$
E_{\...
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In molecular mechanics, how are van der Waals forces modelled?
In terms of energy, how are van der Waals forces modelled (are there formulas/laws that govern these)?
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