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1:20 AM
Q: How I can analyze and present docking results?

Anastasia01I did a docking job and got a score of -5.69 kcal/mol and a value for MM-GBSA of -60 kcal/mol. I should analyze these results for my thesis but do not know how to comment on them. Does anyone have any insight about what this number might mean? Also on interactions, I wonder what can be said? A...

Q: Should I buy a CPU or a GPU for doing calculations?

user1420303A few years ago there was a significant difference between CPUs and GPUs for performing calculations. It was quite clear when to go for a CPU or a GPU. Today there are GPUs with a very large number of cores and threads. I was away from the subject for a while. Is there still such a marked diff...

Q: How to export a calculated Raman spectrum in Q-Chem, as a Gaussian profile?

Dmitry EreminDoes anyone know how to export a calculated Raman spectrum (my calculation was performed in Q-Chem) as a data-file, which can be used to plot the profile of a Gaussian-shape spectrum (in origin, excel, etc.), rathe than centroid data points?

Q: Is there any definitive evidence that implicit solvation methods are more accurate than explicit solvation methods for free energy calculations?

Charlie CrownI am looking for real data that concludes that implicit solvent models are definitively better than explicit solvent models for solvation free energy calculations. The motivation is a lovely reviewer who has said this. Evidence that they are not statistically different is also valid.

Q: How is the material $\ce{\alpha-NaMnO2}$ pronounced?

taciteloquenceI am a theoretical physicist, so I am not very familiar with chemical names. The material I am interested in is $\ce{\alpha-NaMnO2}$. Would that be pronounced alpha sodium manganese dioxide? Is it important to say the $\alpha$? If it's relevant, I'm talking about Phys. Rev. Lett. 2020, 124 (19),...

Q: Converting adsorption binding energy to absolute temperature

CampsThe binding interaction energy during the adsorption of system B on system A can give an idea if the interaction is favorable (negative value) or unfavorable (positive value). Also, the absolute value represents the strength of the interaction. To determine the binding energy, the procedure is t...

Q: I am a beginner in DFT. What are some resources that could help me to learn the basics?

sonia raniI am a beginner in DFT. Please suggest me some good material to understand the basics.

Q: How to "get my feet wet" in Density Functional Theory by simulating a water molecule using Python

uhohI just saw I am a beginner in Density Functional Theory. What are some resources that could help me to learn the basics? and it reminded me that few years ago I'd asked How can I calculate the charge distribution of a water molecule? in Chemistry SE. There is some excellent advice there, but at ...

Q: How to write my own density functional theory (DFT) code in Python?

ThomasI am a DFT user and at some point in the future, I would like to write my own DFT code in Python to help gain a deeper understanding of DFT. As mentioned in a previous answer people have written their own DFT codes to understand more deeply how the theory and algorithms work. Where do I start? ...

Q: Is there a performance difference when using fractional coordinates instead of Cartesian coordinates?

CampsIn general, the CIF file with the crystal structure uses fractional coordinates for setting the atoms positions. In this type of coordinates, the atom positions are relative to the cell parameters. Another way to setting up the atom positions is to use Cartesian coordinates. In this type of coo...

Q: CCSD(T) Transition State and Ground State Calculations in Gaussian09: "Unable to Determine Lambda"?

QuantumXI’m doing CCSD(T) calculations (for both transition and ground state geometries) on a series of small molecules in Gaussian09. Several similar calculations terminated without any problems but one TS calculation and one ground state calculation gave me this error after about 20 minutes. HESSIAN D...

Q: What are the "smart algorithms" applied in computational chemistry to solve the "curse of dimensionality" problem?

Paulie BaoThe "curse of dimensionality" is an ubiquitous issue arise in both electronic structure and quantum molecular dynamics in computational chemistry, which refers to the exponential scaling of the computational cost for the systems of interest as the the number of their degrees of freedom. This...

Q: How to calculate energy of a molecule in an aligned electric field?

EzzeSo I am aware that many quantum chemical codes are able to add external fields to molecular calculations (for example to calculate polarizabilities). I also know that in some (eg. Orca) you have some control over the applied field, for example the strength. I am also aware that for example in Mol...

Q: Is there any software that is optimized specifically for QM/MM?

Charlie CrownA lot of codes can do Quantum Mechanics/ Molecular Mechanics (QM/MM), and I am not naively asking if there is a program that can do QM/MM. What I am interested in is a program that is purely QM/MM meaning that it is designed and optimized specifically for this purpose. QM/MM is not an after-thou...

Q: Is it possible to use the Parrinello-Rahman barostat for NPT simulations in CP2K?

Rashid RafeekIt is possible to use different types of thermostats in CP2K by specifying them in the corresponding section of the input as mentioned here. But there is no mention of specifying the barostat type in the manual. And I couldn't find any mention of the type of barostat being used in CP2K for NPT si...

Q: Labeling of high symmetry points in Brillouin zone

CampsA Brillouin zone is defined as a Wigner~Secitz primitive cell in the reciprocal lattice [1,2]. The construction of the first Brillouin zone for two different 2D lattices are shown below: The construction procedure for 3D lattices is basically the same as for 2D lattices. In the image below, ...

Q: Predicting linear dependencies in a basis set in advance of calculating any integrals

Nike DattaniI've been doing some calculations for a water molecule, with a big uncontracted basis set: For oxygen I am using aug-cc-pV9Z supplemented with the "tight" functions from cc-pCV7Z. The s-type exponents are listed below, with all numbers up to 0.04456 constituting the s-type exponents of aug-cc-pV9...

Q: How does the Hartree-Fock method improve on Hartree after considering the wavefunction that takes the anti-symmetry property into account?

sonia raniI am not able to understand the math of this. After taking the Slater determinant as a wavefunction in Hartree-Fock, does the procedure to find wavefunctions remain the same as in the Hartree method i.e. the self-consistent method, or does it change?

Q: Difference between Van der Waals (DFT-D and DFT-D3) corrections in ab-initio calculations

livars98In Kohn-Sham DFT calculations, Van der Waals corrections are often implemented in the structure optimization calculations because the typical functionals such as LDA and GGA are found to not treat long-range dispersion forces faithfully. But even in the context of Van der Waals corrections, there...

Q: Materials Modeling with Raspberry Pi?

Charlie CrownDoes anyone have any knowledge or direction for creating a homemade Beowolf cluster for materials modeling?I would like to be able to run my own "hobby" simulations at home, so a low energy, low capital investment is what I seek. Raspberry Pi and ODroid use small, cheap, low energy single board c...

Q: How much does the initial geometry affect the final geometry in optimization calculations?

CavenfishThis might be a stupid question but to what extent will the initial configuration of a bulk phase geometry optimization calculation affect the final geometry? Most places say to start with experimental data but if there isn't any then is there a next best way of starting? Would populating your i...

Q: How to calculate the conformational entropy of a molecule?

CampsIntroduction It is know that the entropy of a system can be calculated using the formula (1): \begin{equation} \label{eq:entropy_Boltz} S = {k_B}\ln \Omega\tag1 \end{equation} where $k_B$ is the Boltzmann constant, $\Omega$ is the number of microstates of the system and $S$ is its entropy. Thi...

Q: Spin–orbit interaction with DFT

DiscipleI'm new to DFT. Does the DFT take into account the spin-orbit interaction? On the one hand, this is a relativistic effect, perhaps DFT does not take it into account. However, on the other hand, I read that DFT is an extremely accurate method and the error of this method lies only in the inaccura...

Q: One-center two-electron integrals between 1s STO

ipcamitAs per @user1271772 's suggestion I am asking this question here again. I am trying to understand SCF cycle by trying to code up solved example from Quantum Chemistry by Levine (page 443, 5th edition). The problem is stated as: Do an SCF calculation for the helium-atom ground state using b...

Q: Copyright war: preprint servers vs journals transfer

CampsThis questions is not directly related to Matter Modeling, but it is related with the way we share/publish our research. Let suppose that someone deposited a manuscript in a preprint server. Then, he/she send the same manuscript to a Journal and it is accepted. In many journals you have to sign ...

Q: Is the DYNAMO code developed by LAMMPS still available?

SaiSmaran S B PES1201701189PESIn 2013 it was stated that v8.8 of DYNAMO was the version mostly used for the last 10-12 years. However I am struggling to find the code repository. It was developed by the LAMMPS developers and is used to mix eam potentials. DYNAMO was available on, but now it seems to have be...

Q: What are the advantages of plane wave basis?

Paulie BaoFor systems with periodic boundary condition , plane wave basis is usually adopted. While for molecular systems, gaussian basis set is normally adopted. For periodic systems, the gaussian basis is transformed from real lattice space to momentum space (or k space) through Bloch function. My questi...

Q: The correlation energy from frozen natural orbtials (FNOs) using CCSD and MPBT(2)?

WychhIn other works and from the paper: Scaling Up Electronic Structure Calculations on Quantum Computers: The Frozen Natural Orbital Based Method of Increments. I have seen that the corrected CCSD correlation energy ($E_{c}^{CCSD}(corrected)$) is calculated from a CCSD computation of the truncated...

Q: Is the electronic band gap the only thing that is affected, when switching from standard KS-DFT to Hybrid functionals?

livars98It is very well known that Kohn-Sham DFT underestimates bandgap. To get an accurate estimate of the bandgap, people often turn to Hybrid functionals (if they don't want to perform the actual quasiparticle calculation). I understand how the Hybrid functional, say for example, HSE works. It is an a...

Q: MM-GBSA from Induced Fit Docking on Maestro

Anastasia01How can an MM-GBSA(molecular mechanics energies combined with generalized Born and surface area continuum solvation) calculation be done from an induced fit docking (IFD) output? I performed an IFD and now I would like to run an MM-GBSA calculation, but when I try to start it, I get a warning mes...

Q: Molecular Dynamics simulation software for Windows

Papia ChowdhuryIs there a Windows-based Molecular Dynamics simulation software which is easy to use?

Q: Which Linux distribution is best for Matter Modeling?

ksousaIn some science fields there are efforts to provide customized distributions, so you can get a productive environment with minimum set-up overhead. For example, in high energy particle physics, we have Scientific Linux, in mathematics we have MathLibre, and in cybersecurity research we have Kali ...

Q: Given that Kohn-Sham DFT is strictly a ground-state method (at 0 K), how is it sufficient to describe materials in real-life applications?

livars98Kohn-Sham DFT appears to be so popular even though it is strictly a ground-state method - all calculations are done at 0 K. How then, is it so popular when describing materials that have real-life applications (possibly at room temperatures, or much higher temperatures)? Or am I mistakenly deemin...

Q: Hartree-Fock density vs Kohn-Sham density

QMlabHartree-Fock density is free of self-interaction but lacks electron correlation effects, while the density from KS-DFT (using an xc functional or potential, both which are explicitly density-dependent and gradient-dependent) suffers from self-interaction errors but does incorporate electron corre...

Q: Is the original structure invalid if it's found later that the material crystallises with a slightly different space group symmetry?

ThomasI am studying a material which was first discovered in the early 1960s. It was reported then that it crystallized in the hexagonal $P6_3/mmc$ space group. Recently the material was synthesized again and found that it posses $P6_3mc$ symmetry. My own DFT calculations and another published work fin...

Q: Total spin and/or multiplicity for transition metal ions?

anneb101I am trying to input various charge states of various transition metal ion species into DFT calculations. The program requires an input of multiplicity = 2*(total spin) + 1. I have an undergraduate-level understanding of chemistry, up to the point where I understand orbital filling (1s,2s,2p,.....

Q: conceptual problem about the energy band along the High symmetry point in the Brillouin zone

JensenPangWhen we calculate the band structure of certain material, we only have to calculate the value along the high symmetry point which enclose the Irreducible Brillouin Zone. Why the information lie in the IBZ is enough for us to know the information of entire BZ ? How to find the IBZ given a reciproc...

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

SufyanI 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 require highly involved computational tools (read DFT) to be a bit difficult to explain to these 1...

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

Achintha IhalageI am using VASP package to model a material that has fractional site occupancies. An appropriate supercell (cif) was generated using supercell package and converted to POSCAR using VESTA. Then the structural relaxation was performed. Now I have the relaxed structure (CONTCAR) and I want to analyz...

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

Dmitry EreminI 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 frequencies in frequency calculations. All calculations were performed with SMD(water) (Geometry Optim...

Q: 9 x 9 x 9 periodic xyz file to cif file format

Dong gi KangI 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)

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

livars98I 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 a material might not exist, but in theory, is this true? I am aware that nothing is perfectly ex...

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

Firman(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 and Appropriately Normed) functionals' constraints, but apparently they are not very obvious from t...

Q: Plotting of natural bond orbitals (NBOs)

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

Q: Calculating binding energy between two systems

Shahid SattarRegarding 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 the single point energy of the relaxed complex AB. However, the calculation of $E_A$ and $E_B$ can...

Q: Docked pose and energy minimization

BNDIs 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 affinity? Does someone have some published literature on that?

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

Achintha IhalageI 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 arrangement (visualised in VESTA) when looked along the Z axis. One of the ways to model such structures i...

Q: Software to draw 3d micelle configuration

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

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

ksousaI'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 find comparisons like these, but updated often, or at least more recently? I specified quantum che...

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

ksousaSome 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 multiplication in $N \log N$ steps. Compare with the $N^2$ we are used to while doing multiplicati...

1:37 AM
Nike Dattani has made a change to the feeds posted into this room
1:56 AM
Q: Was Walter Kohn wrong about this?

ProfMIn 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, when $N\geq N_0$ where $N_0\simeq10^3$." He explains this in two ways: the first is that $\Psi$ cann...

Q: Why is the band gap of graphene "opened" in this VASP calculation?

JensenPangI 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 when I zoom in the region where the conduction band touches with the valences band, a bandgap can...


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