# All Questions

366 questions
Filter by
Sorted by
Tagged with
40 views

### How to properly design a modeling experiment? [closed]

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 ...
120 views

### Ab initio molecular dynamics to check material stability at finite temperature

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 ...
25 views

### Calculate spin-spin coupling based on previous GIAO calculation with Gaussian

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 ...
156 views

### Semi-infinite surfaces for adsorption: a valid approach?

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 ...
34 views

### How do I generate an aluminum force-field for a LAMMPS input file?

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 ...
731 views
+100

### What are the different types of charge analysis?

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 ...
102 views

### How to convert from primitive to conventional after structure relaxation?

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, ...
61 views

### What is the speed/time required for DFT simulations?

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 ...
158 views

### How can I scan the whole PES of a bulk structure?

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

### A CCSD(T) geometry optimization in Gaussian09 is deviating too far from the minimum. How do I deal with it?

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 ...
389 views

### Create a new DFT functional from experimental data

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 ...
179 views

### How to map the electrostatic potential from GAUSSIAN, on a solvent accessible surface?

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. ...
79 views

### Why can't I reproduce the behavior of an H-saturated graphene flake?

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. ...
2k views

### What is the cutting edge for open-source Force-Field generation?

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 ...
45 views

### Poiseuille flow by LAMMPS

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 ...
61 views

### Correlation Functions in the Cluster Variation Method

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 ...
48 views

### How to convert a molecular structure made in Avogadro to a LAMMPS coordinate file?

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 ...
206 views

### Why is the band gap of graphene “opened” in this VASP calculation?

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 ...
1k views

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,...
683 views

### What is the most user friendly software for frequency visualization rendering?

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. ...
27 views

### nanoparticle synthesis by precipitation methods [closed]

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

### How to rectify the error “Lost atoms: original 28437 current 3659” in LAMMPS?

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 ...
443 views

### Meaning of atomic positional parameters

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 ...
102 views

### How to convert Unified Pseudopotential Format (UPF) into Ultrasoft Pseudopotential (USPP) format?

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 ...
63 views

### What is Gaussian16's read-file logic when using ONIOM with genecp?

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

### 3D Poisson equation solver for arbitrary charge distribution?

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 ...
49 views

### What are the steps to prepare a solid-solid interface for adsorption studies in plane-wave DFT?

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.
223 views

### What are the applications of chemical graph theory?

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....
127 views

### The Hund's J - Why can this be quantified?

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 ...
6k views

### Did the 2019 discovery of O(N log(N)) multiplication have a practical outcome?

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 ...
156 views

### Is there a set of updated, comprehensive benchmarks for speed comparison between different quantum chemistry packages?

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 ...
72 views

### How to characterize surface features in proteins?

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 ...
104 views

### Software to draw 3d micelle configuration

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

### How does the atomic arrangement look like in a compound that has partial/mixed site occupancies

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 ...
85 views

### Docked pose and energy minimization

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 ...
44 views

### How to generate relativistic pseudo-potential using Vanderbilt USPP that captures spin-orbit coupling?

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 ...
107 views

### Calculating binding energy between two systems

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 ...
55 views

### Conductivity Computations of Molecular Wires [closed]

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.
480 views

### Plotting of natural bond orbitals (NBOs)

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

### Mathematical expression of SCAN (Strongly Constrained and Appropriately Normed) constraints in DFT

(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 ...
205 views

### Can DFT be 'exact' in the limit of the uniform electron gas?

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 ...
395 views

### 9 x 9 x 9 periodic xyz file to cif file format

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)
66 views

### Which SCF energy to use to plot PES after calculations with SMD?

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 ...
100 views

### What are the ways to ensure thermodynamic stability of a DFT modelled new structure?

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 ...
23 views

### Converging the potential of a dilute binary alloy system using the Coherent Potential Approximation. What troubleshooting options could I take?

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....
210 views

### How to analyze the space group of a relaxed structure that has fractional site occupancies

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 ...
649 views

### How would you explain Density Functional Theory to a high school student?

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 ...
47 views

### Is there any way to semi-quantify antibacterial/antimicrobial properties of a material using DFT?

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 ...