10

Electrostaic embedding is usually on the QM-side as simple point charges which add to the total hamiltonian of the nuceli+electrons. It should be just a simple coulumb interaction. Any modern electronic structure calculation software should support aleast electrostatic embedding. Openmolcas, Orca, Dalton/LSDalton, Bagel all support electrostatic embedding, ...


8

The fluctuation volume $\langle\Delta V^2\rangle$ is the variance of the volume V, defined as the squared distance between V and the average volume $\langle V \rangle$, averaged over the trajectory: $$\langle\Delta V^2\rangle = \langle(V - \langle V \rangle)^2\rangle$$ It can easily be computed with the following equivalent formula, where $\langle V^2 \...


8

If I understand your question correctly, you are saying that you have seen cases where time is included in the calculation of the radial distribution function (RDF). The RDF itself does not depend on time (and its calculation does not depend on any timestep). That is, the RDF is calculated as an ensemble average, so that either molecular dynamics or monte ...


7

Your problem comes from the line: fix 11 A print v_com "coords of center of mass" file cdm.dat As per the documentation, the correct syntax is: fix ID group-ID print N string keyword value ... Where it will print every N timesteps. So you are asking LAMMPS to print the same message every v_com timesteps. And LAMMPS is respectfully ...


6

Other answers explaining Nyquist's Sampling Theorem are completely correct. Read those before mine. I'd like to add some information about how details of how you run your simulation can affect the Nyquist frequency, and therefore, in practice, affect the fundamental question of how to choose your time step. As one can easily imagine, tricks that let you ...


6

Having read the above answers I think it's important to point out why you generally use a time step below the upper limit provided by Nyquist's Theorem. The theorem itself describes the maximum number of signals it's possible to send through a telegraph cable and still have them be discernable from one another. That makes the limiting case a sampling ...


6

vkj's answer addressed the third part of the question. I'll answer the first part. Which quantum chemistry methods can be used in an external electrostatic field? Also which software supports that? I'm interested in anything from semiempirical (eg XTB) to DFT (eg ωB97, B3LYP-D3) to coupled cluster (eg DLPNO-CCSD(T)). The only starting point I have is a few ...


5

I don't think you can build a nanoparticle using Avogadro, I personally use ASE which is a python package that can output a lot of different formats (xyz, cif, vasp, ...) You can directly output LAMMPS format using ASE or you can use Atomsk to convert whatever format to LAMMPS. By doing that you will obtain a "lammps-data" file, which needs to be ...


4

Following Nike and Tyberius's suggestions, I rewrite my comment into an answer. Firstly, it is obvious that when the volume of the simulation box is sufficiently large, then a significant fraction of the box must be gaseous. Secondly, note that the simulation box has a finite size, so that when the equilibrium pressure of the gas is sufficiently low, it may ...


4

You can either use python or MATLAB to generate the coordinates, or even use the built in tools in LAMMPS. To do this in LAMMPS, you only need to follow three steps. Use the lattice command to define the lattice type (diamond for Silicon) "https://docs.lammps.org/lattice.html". Use the region command to define a region with the desired dimensions....


2

Atomsk You can use this software to play with the structure and then, generate de coordinate file for you program. Atomsk is a free, Open Source command-line program dedicated to the creation, manipulation, and conversion of data files for atomic-scale simulations. It supports the file formats used by many programs, including: Visualization and analysis ...


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