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4
votes
0answers
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 ...
13
votes
1answer
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 ...
9
votes
0answers
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 ...
14
votes
1answer
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 ...
5
votes
0answers
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 ...
20
votes
8answers
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 ...
13
votes
1answer
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, ...
11
votes
0answers
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 ...
12
votes
1answer
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.
10
votes
0answers
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 ...
18
votes
2answers
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 ...
14
votes
1answer
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. ...
16
votes
1answer
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. ...
13
votes
2answers
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 ...
10
votes
0answers
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 ...
11
votes
0answers
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 ...
12
votes
0answers
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 ...
12
votes
1answer
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 ...
29
votes
1answer
1k views

Was Walter Kohn wrong about this?

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,...
10
votes
2answers
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. ...
1
vote
0answers
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?
12
votes
1answer
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 ...
17
votes
2answers
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 ...
10
votes
2answers
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 ...
11
votes
1answer
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 ...
11
votes
1answer
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 ...
10
votes
0answers
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.
16
votes
6answers
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....
14
votes
1answer
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 ...
56
votes
6answers
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 ...
13
votes
1answer
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 ...
14
votes
1answer
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 ...
9
votes
1answer
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?
12
votes
1answer
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 ...
8
votes
2answers
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 ...
8
votes
1answer
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 ...
16
votes
2answers
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 ...
5
votes
1answer
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.
11
votes
5answers
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?
17
votes
1answer
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 ...
12
votes
1answer
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 ...
11
votes
3answers
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)
9
votes
2answers
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 ...
14
votes
1answer
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 ...
10
votes
0answers
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....
11
votes
3answers
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 ...
13
votes
3answers
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 ...
12
votes
1answer
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 ...
2
votes
0answers
64 views

Materials Modeling in Industry [closed]

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) ...
7
votes
1answer
56 views

Is there a relation between self-interaction errors and integer-discontinuities in Kohn-Sham-DFT?

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

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