All Questions
2,232
questions
2
votes
0
answers
17
views
Tools for working with tight-binding models
I would like to analyze a Slater-Koster tight binding model for some materials. I have the data for both the Hamiltonian as a matrix-valued map on the reciprocal lattice $H_{mn}(\vec{T})$ and the ...
- 61
4
votes
0
answers
33
views
Is it possible to build a force field that suits all elements based on vasp's machine learning result?
I have tried to use VASP's machine learning force field calculation during running molecular dynamics simulation with a supercell including some elements of Ti, O, Cu, etc. It does increase the speed ...
- 1,427
7
votes
1
answer
122
views
QuasiRRHO in Orca
I read that ORCA runs a QuasiRRHO calculation based on Grimme approximation, at the end of a freq calculation.
Unfortunately, I wasn't able to find the default value for the CutOffFreq. In Grimme's ...
6
votes
0
answers
22
views
Is the HOMO energy obtained from GW calculation always a value relative to the vacuum energy (-Ip)?
Aim:
I want to obtain a reasonably accurate ionization energy (or work function in other terms) for a 2-dimensional hBN monolayer. The exact material does not matter much respective to the question, ...
- 161
3
votes
0
answers
27
views
What is the curve fitting model used for Qubit protein assay?
This is the example of Qubit protein assay curve.
It relates the concentration (x-axis) with fluorescence (y-axis).
What is the curve-fitting method it use for this?
Clearly this is not simple linear ...
- 1,492
3
votes
0
answers
27
views
Coulomb energy in VASP
In DFT, the Coulomb energy is defined as the sum of Hartree energy, nuclear-electron attraction, and nuclear-nuclear repulsion. In VASP output, we can find the Hartree energy, and also the nuclear-...
3
votes
0
answers
33
views
Rys Quadrature method for integrating over Gaussian basis functions: 1D integral recursion relation
I'm trying to implement the Rys Quadrature method for integrations of Gaussians, from scratch. I'm using this paper as a reference.
So, how does the overall recursion relation for evaluating 1D ...
- 123
3
votes
0
answers
27
views
Green function KMS boundary condition
How to obtain the relation between $G_{ab}(\tau,0,0,0)$ and $G_{ab}(\beta-\tau,0,0,0)$ for two-particle fermion Green function
$$G_{ab}(\tau_1,\tau_2,\tau_3,\tau_4)=\langle \mathcal{T}a^\dagger(\tau_1)...
- 91
6
votes
0
answers
62
views
Analytical derivative method in ab initio molecular properties calculations
In order to relate results from quantum chemical calculations to experiment, it
is essential to compute quantities that are directly available from measurements.
Properties describe the "response&...
- 357
5
votes
0
answers
84
views
Definition of the terms "modeling" and "simulation" in the context of biomolecules and/or proteins
What are the definitions of the terms "modeling" and "simulation" in the context of biomolecules and/or proteins?
Examples will be highly appreciated.
Also, please, back them up ...
- 603
6
votes
1
answer
87
views
How exactly are valence orbitals combined in split valence basis sets such as 3-21G?
For hydrogen, the 3-21G basis set (in CFOUR format) is
...
- 161
9
votes
1
answer
231
views
How to build cartesian representations of spherical Gaussian basis functions?
I'm trying to code an integral library for my own QC software from scratch. I need to use the spherical basis functions like in any other popular program. So, a D basis function is supposed to make ...
- 123
7
votes
2
answers
184
views
What does it mean by "transferable" in the case of a force field?
According to Wikipedia:
Functional forms and parameter sets have been defined by the developers of interatomic potentials and feature variable degrees of self-consistency and transferability. When ...
- 603
3
votes
0
answers
56
views
What are the similarities between MD and MC in the case of protein simulation?
As far as I understand, both MD and MC simulation methods use Force Fields.
Are there any other similarities between them?
- 603
2
votes
0
answers
40
views
What do we simulate with molecular simulation of proteins?
I know some:
Secondary structure prediction
Tertiary structure prediction
protein-surface interaction test
protein-protein interaction test
protein-ligand binding test
What else do we simulate?
...
- 603
0
votes
0
answers
38
views
Academic help on the use DFT for modelling [closed]
I need help on the knowledge of DFT for semiconductor modelling/fabrications, from the scratch. I'm ready and willing to be your student please.
4
votes
0
answers
23
views
Radius of gyration and aggregates
I have performed a MD simulation using GROMACS for a system of 100 caffeine molecules in water. It is expected caffeine form aggregates.
I have calculated the radius of gyration for the simulation ...
- 41
2
votes
0
answers
30
views
Why does the GPU version of VASP consume a lot of time on STRESS calculation?
I am trying to compare the CPU and GPU versions of VASP.6.3.0, it seems that the GPU version consumes a lot of time on the STRESS item, does it represent the time for calculation stress tensor?
Here ...
- 1,427
-1
votes
0
answers
40
views
Average of last 5000 steps
I am trying to use fix ave/time with start to get the average of the last 5000 steps of my 100,000 step simulation. I tried this ...
6
votes
0
answers
70
views
Is there a system of multiple interacting quantum particles for which density can be obtained analytically?
I know that it is impossible for real electrons and nuclei. In the Kohn and Sham approach, a system of interacting electrons is approximated by a system of non-interacting Kohn-Sham particles in an ...
2
votes
0
answers
25
views
How do I find out the subdivisions N_1, N_2 and N_3 in BAND STRUCTURE?
I want to find out how to get subdivisions from vasprun.xml of Brillouin zone. Does anyone know how to do this?
- 61
3
votes
0
answers
26
views
Calculating the Diffusion coffecients from Trajectory file in ASE
I plan to study the Diffusion-Coefficient of my simulation outputs, for this, I want to use ASE.
Sadly I am not entirely sure of how to proceed, has anyone done this and if yes, please share your ...
- 715
1
vote
0
answers
35
views
Interlink among different length scales of simulation and modelling techniques
I found this figure:
In the following paper:
A Review on Multiscale Modelling and Simulation for Polymer Nanocomposites
However, I am skeptical about its correctness, as this paper is not peer-...
- 603
3
votes
0
answers
38
views
Is the 4-index tensor in the coupled cluster code of PySCF stored in memory or on disk?
In the coupled cluster code of PySCF, is the four index tensor stored in memory or in disk?
- 3,629
1
vote
0
answers
10
views
Getting some errors while extracting the data for phonon band strucutre
I am getting some errors while extracting the data for phonon band structure:
...
4
votes
2
answers
472
views
Which formalism is better suited to model a crystal with defects: Hartree–Fock, Kohn–Sham, or something else?
Let’s suppose that
(1) it’s required to calculate a crystal with certain parameters of a crystal lattice;
(2) this crystal has some defects (let it be Frenkel defects for simplicity);
(3) these ...
- 91
2
votes
0
answers
22
views
What does it mean if the Fermi level crosses into the valence band? How about into the conduction band?
Just recently got into DFT and I've been doing a few calculations on my own on Quantum Espresso. I've come up with electronic band structures for materials that I've been looking at and I was hoping ...
- 161
7
votes
0
answers
87
views
What is the best cell shape to calculate the energy of a free atom with a periodic DFT code (VASP)?
I want to study the adsorption energies of many different atoms to some surfaces. For that, I need to calculate the energies of free atoms (adsorbates) in a vacuum.
I understand that I am supposed to ...
6
votes
0
answers
42
views
How to run 2nd generation CPMD in CP2K?
I believe CP2K by default implements Born–Oppenheimer MD. I have seen many recent papers that use 2nd generation Car–Parrinello MD using CP2K. But I couldn't find any direct way of switching to 2nd-...
- 1,541
3
votes
0
answers
24
views
Computing a reaction barrier from a Metadynamics simulation
I've been conducting Metadynamics runs for an interfacial reaction in order to calculate the forward barrier. Others have taken the first barrier crossing energy as the true barrier. In my system, the ...
- 81
4
votes
0
answers
32
views
Are multiplet free atoms multireference?
In general, my understanding is that free radicals and non-equilibrium molecules sometimes need multireference electronic structure calculations, mainly because of different electronic states being ...
5
votes
1
answer
205
views
Scalar relativistic Calculation for pseudopotential
I am new to solid state calculation. I have a question about the pseudopotential in terms of the relativistic effect. In solid-state calculations, ultrasoft pseudopotential using PBE functionals are ...
- 111
4
votes
0
answers
29
views
How to install a package on MacOs?
I have installed LAMMPS on my mac-pro (OS Monetery), using the following link:
https://docs.lammps.org/Install_mac.html
so first I installed homebrew and then lammps. I need to install DPD-REACT ...
4
votes
0
answers
30
views
Benchmarks for optimised Math Libraries across platforms
Are there any benchmarks of low-level and high-level math operations from different Math libraries on corresponding architectures?
Here are a few packages:
LAPACK / BLAS + ATLAS (stock version from ...
- 905
3
votes
0
answers
39
views
Domain decomposition error while applying bonded restraints
GROMACS version:version 2021.3-MODIFIED
GROMACS modification: Yes
Hi, I have a small system with 87 residues of a protein. And I want to maintain the tertiary structure of the protein, so I came up ...
- 974
5
votes
1
answer
48
views
How to create the vector image of crystal structure?
I am trying to create a vector image of TiO2 crystal because all journals require vector images. When I build the model for calculation, I use ...
- 1,427
6
votes
1
answer
132
views
Raman Spectra in Quantum Espresso
Does anyone have any experience simulating Raman spectra in Quantum ESPRESSO? Following the example 15 that comes with QE, I have attempted to simulate the Raman spectrum of MgO. I know the lraman ...
- 91
5
votes
1
answer
49
views
How are the exponents in a STO-nG basis set obtained?
STO-3G has exponent parameters which can be found in a reference book. Can these parameters be calculated using, for instance, a Hartree–Fock equation for one atom? Or using another way?
- 91
4
votes
0
answers
44
views
Regarding use of GCMC to add water molecules
I am working on a goethite system, and wish to fill the unit cell with water molecules for AIMD simulation using quantum espresso. For this, some papers[1],[2] indicated the use of Grand Canonical ...
- 557
1
vote
0
answers
10
views
How to select NBANDSO and NBANDSV and NBANDS values in BSE GW calculation in VASP
I am not aware of how to select NBANDSO and NBANDSV and NBANDS values in the 5th step while doing the BSE calculations. Please suggest.
0
votes
0
answers
26
views
Open issues in MC protein simulation?
What are some open issues in Monte Carlo protein simulation research?
I am especially interested in coarse-graining.
- 603
4
votes
1
answer
93
views
Future and limitations of DFT
I'm a graduate student beginning research in condensed matter physics. Naturally, I am very interested in mathematics. I am aware that, in condensed matter physics, theorists employ tools from pure ...
- 61
4
votes
1
answer
67
views
Why I have difference between DOS and BAND gap?
As they advise everywhere, SKF should be considered without SOC, and already in NSCF, spin-orbit interaction should be included. But what is the actual question, as I know, band splitting occurs with ...
- 61
5
votes
0
answers
32
views
How to get hydrogen indices in RDKit substructure matches
I am searching for functional groups in RDKit molecules and want to get the corresponding atom indices. Using GetSubstructMatches() however does not return some (...
gloomy5k
5
votes
1
answer
60
views
Successfully running parallel gas phase calculation on AMD cloud instance but implicit solvent fails (Local Intel workstation successfully runs both)
I am using an AMD Linux cloud-based instance to ran general optimisation and transition state calculations in parallel. I have noticed that I can run gas phase calculations in parallel but the run ...
- 81
4
votes
0
answers
22
views
How to download METADISE code?
I have a (possibly trivial) question regarding the METADISE code. I can find the documentation related to this code, but I cannot find the download page/tarball anywhere.
Can someone kindly share any ...
- 557
8
votes
4
answers
1k
views
DFT code for simulating thousands of atoms in a supercell
I'm trying to simulate a supercell that contains thousands of atoms with the DFT method, but it seems VASP couldn't handle such a large system, its parallel efficiency is relatively low, when I try to ...
- 1,427
7
votes
0
answers
54
views
How to choose K point for a super cell
I have been told to use VASPKIT in order to obtain the KPOINTS, but VASPKIT only works for Primitive cell and I am currently using a super cell. The super cell has a repeated primitive cell about one ...
- 1,387
3
votes
0
answers
23
views
Is the energy due to external electric field included in gromacs energy?
I have a Gromacs NVT simulation with a constant external electric field using the option "electric-field-z = 1.5 0 0 0".
When calling gmx energy -f (...).edr to calculate the potential ...
- 131
6
votes
0
answers
37
views
density of state with spin orbit coupling
I have been doing DOS calculations with SOC tag on in VASP, and another calculation without SOC. As shown in the figure the DOS with SOC seems strange! is this wrong? How can I have resolved
I have ...
- 455