All Questions

How can someone properly decide on an appropriate level of theory MM, QM... What are the checklists throughout the experiment (in-silico)? How to decide a proper control case/group? For example from ...

I completed an ab initio molecular dynamic (AIMD) simulation in VASP for a hypothetical material. The simulation was done for 5ps with 1fs steps and the temperature was set to 300K using Nosé–Hoover ...

I used GAUSSIAN/GAUSSVIEW to calculate the GIAO Magnetic shielding tensor (ppm), but I forgot to calculate the Nuclear spin-spin coupling J (Hz). How can I use the .chk file or .log file to calculate ...

I'm currently trying to surface reaction of small molecules on metal oxides in VASP. Several papers I've read have approached surface energy calculations in a variety of ways. I first began looking at ...

I have been assigned a project on the generation of a force-field of Al (aluminum) for a LAMMPS potential. I have no idea how to proceed and what to do next. Can anyone please let me know how should I ...

I am evaluating the atomic charge of an IP system and comparing with a DFT system by using three different charge analysis methods (Mulliken, Bader, Qeq). I wonder what are the differences between the ...

I did this in VASP but I guess this would be the case for any program. I have a structure that has a cubic conventional cell (a = 9.86 A). I found the primitive cell (a=b=c=6.97, alpha=90, beta=60, ...

I am currently designing a toy model to calculate an interatomic potential (for an infinite repeating lattice) this toy model needs to scale and perform better than DFT simulations. But sadly I have ...

I am not very familiar with scanning a PES for a bulk structure, and I'd be very appreciative for some suggestions.

I am doing a CCSD(T) geometry optimization on a series of molecules. One of the geometry optimizations took about 2 weeks even though an analogous molecule with the same number of basis functions took ...

This is my first time here and I think you can help me. I would like to try (just for fun) to create a new DFT functional starting from experimental data. Do you have any manual, procedure or ...

Gaussian cubegen and surface generators in Gaussview seem to only allow to map the ESP on SCF densities. I used G16 for the ESP generation. I would like to plot it on the solvent accessible surface. ...

I'm trying to simulate a graphene flake with its edge C atoms saturated by H atoms, in a temperature ramp from 300 K to 1600 K, using LAMMPS and the AIREBO potential proposed by Stuart et al. in 2000. ...

The adoption of atom-typing allowed for the creation of incredibly widely used force-fields (FF) such as GROMOS/AMBER/OPLS and many more. Because of the assumptions ...

I am trying to model 3D Poiseuille flow of an argon gas confined between two parallel platinum plates by using LAMMPS. I have one reference paper, as given in [1] below. I built my platinum structure ...

I've been referring to Dr Mohri's paper [DOI: 10.1007/s11837-013-0738-5] for the cluster variation method (CVM). I wish to calculate the configurational entropy of a binary FCC system. Cluster ...

I was trying to convert a crystal structure into a LAMMPS data file in Avogadro but whenever I type .lmpdat as an extension, it says "The file name is not valid". Can you tell me any ...

I used VASP to do the band structure calculation on Graphene. Originally I would expect that the Dirac cone can be observed in the K point. If we watched qualitatively, we can see this behavior. But ...

In Kohn's Nobel Lecture, he claimed that: "In general the many-electron wave function $\Psi(\mathbf{r}_1,\ldots,\mathbf{r}_N)$ for a system of $N$ electrons is not a legitimate scientific concept,...

I perform my calculations in Q-Chem and would like to make short movies of IR modes. As of now, I render them with IQmol, but I believe graphics properties (colors and resolution) can be much better. ...

nano particle synthesis Anyone about nano particle synthesis by precipitation methods? what are the different precipitation methods?

I have modeled a complex structure of a protein and a Carbon nano-cone (used as an indenter to the protein) using PACKMOL. The LAMMPS data file of the complex structure consists of 4 atom types (C O N ...

I am trying to model some materials with DFT, so I intended to start out with the structure. However, some texts that present XRD data, use a term called atomic positional parameter. I can't seem to ...

I am working on DFT code having plane wave along xy axis and bspline in z direction. For calculating the properties of TMD materials, spin orbit coupling must be included but i did not find fully ...

I want to use the ONIOM keyword, like oniom(ccsd(t)/avtz:m06/genEcp) or similar, in conjunction with genecp. I want to use ...

I am trying to compute the electrostatic potential profile from a distribution of point-charges that were output from an MD simulation. Does anyone know of ready-made Poisson solver packages that are ...

Please, how may one simulate a solid-solid interface that one can carry out adsorption studies from. I tried using virtual nanolab in Quantum ATK but didn't get a hand of it.

Graph theory was originally introduced in computer science to study data structure. Chemists also introduced graph theory to study the relation between structure and properties for molecular compounds....

I was reading on the implementation of Hubbard 'U' in Density Functional Theory. The Hubbard 'U' can be thought of as a parameter that accounts for the on-site electron-electron interactions in ...

Some time ago I've read this news article, Mathematicians Discover the Perfect Way to Multiply, reporting a discovery published in 2019, where Harvey and Hoeven[1] found a algorithm able to execute ...

I've found a page dedicated to quantum chemistry packages benchmarks, on GitHub, qmspeedtest. But most results there are several years old, and so probably outdated. Is there some place where we can ...

When looking at the structure of protein domains I notice many of them show a cleft-like structure in the same location (when aligned to each other). What is a recommended way of characterizing these ...

I am looking for a free software able to draw 3d micelle configuration like the figure attached. Any suggestion?

I am working on modelling of a material that has partial/mixed site occupancies. For example consider the tetragonal (P4mm) compound $\ce{(Ba_{0.67}Sr_{0.33})TiO3}$. Following is the atomic ...

Is it useful to energy minimize a docked pose before scoring it? I am speaking in the context of protein-ligand systems. Does the energy obtained after minimization correlate better with experimental ...

I have used Vanderbilt USPP for generating a pseudopotential that does not include the spin-orbit term. But I want to have the spin-orbit coupling term included in the pseudopotential, to do ...

Regarding the calculation of binding energy of molecular absorption on graphene, for which this has been discussed before, the process of calculating $E_{AB}$ is fairly straight forward, i.e., it is ...

I am interested to compute the conductivity properties of some molecular organic wires in SIESTA. Since I am new in SIESTA, I would appreciate a guide for beginners to this field.

Which quantum chemistry programs can compute natural bond orbitals (NBOs)? Which visualisation tools can I use subsequently to plot pictures of the NBOs?

(This question is originally posted on physics stackexchange, but someone suggested me to post on this site, so there you go) I'm compiling the mathematical expression of SCAN (Strongly Constrained ...

I was wondering if DFT (or specifically, LDA ?) can be exact in the limit of the homogeneous electron gas? In that case, shouldn't the self-interaction error perfectly cancel out? I realise that such ...

I have a 9 x 9 x 9 periodic crystal structure in .xyz format and I would like to change it to .cif file format. Does anyone know how to convert the file? (e.g. 9 x 9 x 9 to unit cell then cif)

I have a series of molecules calculated (DFT PBE0-D3/def2-TZVP performed in Q-Chem) and I'm ready to plot PES (Potential Energy Surface). I had to increase the grid to get rid of small imaginary ...

One way of predicting the thermodynamic stability of a DFT modelled structure is to calculate the energy above convex hull, which was used as the criterion in The Materials Project database. For ...

I'm trying to converge a dilute fcc alloy consisting of Cu and U, with the Uranium concentration at 0.01% and the lattice parameter of Cu, using Hubert Ebert's SPR-KKR program (https://www.ebert.cup....

I am using VASP package to model a material that has fractional site occupancies. An appropriate supercell (cif) was generated using supercell package and converted ...

I find the experiments to be relatively easy to explain to my young cousins (who are planning to take scientific reserach as a career option). I find the theoretical works, especially the ones which ...

As we know, due to the current pandemic situation, people are getting more awake regarding hygiene and health. As such, there are many researches, both computational and experimental, within the ...

This question is primarily targeted to individuals who are working in industries and in the field of materials modeling. [Be ambiguous wherever required] (i) Please explain your role briefly (ii) ...

I am wondering whether or not self-interaction error and integer-discontinuity in Kohn-Sham density functionals, are related to each other?