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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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7 votes
2 answers
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Calculation of the vdW interactions without DFT

I am looking for proxy methods of calculating vdW interactions similar to the DFT-D2, DFT-D3, and DFT-D4 methods which require only atomic positions and/or properties of the atoms. It would be good ...
Tristan Maxson's user avatar
4 votes
0 answers
101 views

How to perform a rotation of a structure, specifically throughout molecular dynamics or umbrella sampling simulations?

I have a structure, as depicted in the figure, which is a part of a longer chain. The portion within the red circle is predominantly parallel. My objective is to rotate this part, aiming to orient the ...
Abd-Elazeem Mohamed's user avatar
4 votes
1 answer
65 views

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 ...
Fadelis Hu's user avatar
3 votes
0 answers
218 views

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: ...
breadcrumbs's user avatar
5 votes
1 answer
175 views

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(...
epalos's user avatar
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3 votes
1 answer
131 views

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 ...
Devanjith Fonseka's user avatar
6 votes
0 answers
55 views

Is it possible to evaluate rotational and vibrational partition functions for diffusion in the Eyring Theory of Absolute Rates? [closed]

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{\...
Giuseppe Basile's user avatar
2 votes
1 answer
56 views

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 ...
jheindel's user avatar
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8 votes
1 answer
292 views

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 ...
user35952's user avatar
  • 343
7 votes
2 answers
192 views

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 ...
SFriendly's user avatar
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4 votes
1 answer
32 views

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 ...
krowney's user avatar
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4 votes
0 answers
89 views

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 ...
Paul Logan's user avatar
7 votes
0 answers
149 views

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 ...
Dario Mirić's user avatar
4 votes
0 answers
64 views

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: ...
fireball.1's user avatar
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7 votes
0 answers
275 views

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 ...
Kavya Mrudula's user avatar
9 votes
1 answer
102 views

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 ...
NTS's user avatar
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14 votes
2 answers
793 views

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 ...
user avatar
6 votes
1 answer
1k views

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&...
Cody Aldaz's user avatar
  • 8,017
6 votes
1 answer
531 views

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 ...
S R Maiti's user avatar
  • 6,991
7 votes
0 answers
84 views

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 ...
Roman's user avatar
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8 votes
2 answers
124 views

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 ...
jheindel's user avatar
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10 votes
1 answer
240 views

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, ...
Shredderroy's user avatar
8 votes
2 answers
148 views

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-...
lewiso1's user avatar
  • 936
8 votes
1 answer
151 views

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 ...
Binh Thien's user avatar
  • 2,095
18 votes
1 answer
382 views

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 ...
geo's user avatar
  • 455
11 votes
1 answer
555 views

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 ...
Safdar Faisal's user avatar
12 votes
1 answer
246 views

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?
anneb101's user avatar
  • 995
23 votes
3 answers
1k views

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 $U_{ij} = \frac{1}{2}k(r_i - r_j)^2$ ...
James Flash's user avatar
15 votes
1 answer
315 views

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 ...
SalvaCardona's user avatar
  • 1,590
22 votes
1 answer
259 views

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 ...
B. Kelly's user avatar
  • 4,366
29 votes
3 answers
4k views

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 $U$. ...
epalos's user avatar
  • 4,869
24 votes
2 answers
471 views

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_{\...
schneiderfelipe's user avatar
36 votes
3 answers
1k views

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)?
TheSimpliFire's user avatar