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7
votes
0answers
28 views

Is there some free software to do some computation of Frank-Condon analysis?

I know Gaussian 16 can do it, but are there some free software to do? For simple excited state calculations using TD-DFT, we can use NWChem and Octopus.
10
votes
4answers
307 views

Are dispersion correction methods for DFT (such as D3) useful for geometry optimization?

For what I know the DFT-D3 method or similar corrections that take into account dispersion effect, add this type of contribution through calculation of atom pairwise interactions at the end of an ...
6
votes
2answers
32 views

LAMMPS data files, making atom IDs contiguous

I sometimes need to remove atoms from LAMMPS datafiles by hand, removing each row that corresponds to an atomID I want to remove, then decrementing the total atom count. This causes the atom IDs to no ...
10
votes
3answers
484 views

Which DFT functional should I use to simulate spectra of pesticides?

I am mainly searching for functionals to calculate spectra of pesticides. I found the benchmark test from Goerigk and Grimme$^1$, but don't understand which of the functionals suits my purpose the ...
7
votes
2answers
98 views

Why is there a large discrepancy between calculated frequency dependent dielectric function and experimental measurement?

I am calculating the frequency dependent dielectric function of $\ce{SiC}$ using VASP. After a geometry optimization, the INCAR file below is used for the ...
6
votes
0answers
17 views

Construction of dimeric protein models, selection and refinement

I want to perform a molecular docking between a protein of interest and several ligands. This membrane protein has a transmembrane domain composed of an alpha helix structure, which exerts it's ...
15
votes
2answers
513 views

What are good tools for visualizing glide planes and screw axes?

While there are a few tools for visualizing crystal structures, I'm particularly curious to know tools for visualizing space group symmetry, including: screw axes glide planes I teach a class on ...
4
votes
0answers
33 views

How to do a Sampling on the boundary of Brillouin zone in VASP

I use VASP to do my DFT calculation. I have to do a self consistent calculation to generate my CHGCAR. I want to ask is there anyway to write the KPOINTS file to generate K-meshing grid which can ...
3
votes
1answer
25 views

Ligand-protein molecular docking with different protonation states

It is known that protonation states of the receptor and the ligand before and after the binding are a very important factor for the binding, as indicated by both experimental data and computational ...
8
votes
0answers
25 views

Protein structure prediction

I want to perform a molecular docking between several ligands and the transmembrane domain of a protein. For this protein I only have the amino acid sequence, so it's necessary to do two things: ...
6
votes
1answer
81 views

How to plot exciton wave function with phase information?

In GW-BSE calculations, people could analyze the exciton wave function $|S\rangle$ by plotting the BSE eigenvector $A_{cv\mathbf{k}}$ that satisfies $|S\rangle = \sum_{cv\mathbf{k}}A_{cv\mathbf{k}}|cv\...
7
votes
1answer
52 views

Calculation of dispersion energies for organometallic complexes with Gaussian

I've tried to calculate dispersion energies of some organometallic complexes with the Gaussian software using WB97XD/Gen (...
5
votes
0answers
27 views

Is it possible to install thermo_pw on windows 10?

For research purpose, my team needs to use thermo_pw package for ab-initio simulations. But the issue we are running into is that we cannot find a way to install it on our computer. We are using ...
5
votes
1answer
126 views

How to calculate state population from MCTDH?

In this reference, the author investigates electronic population dynamics from a MCTDH calculation. My question is how to generate state populations over time from an MCTDH calculation? Is there a ...
7
votes
0answers
49 views

What are some types of topologically-relevant band degeneracies in contemporary 2D condensed matter research?

Cross-posted the question here: https://physics.stackexchange.com/q/633457/49107 In the study of 2D condensed matter systems, I have seen several kinds of band degeneracies. I call 'bands' the ...
19
votes
3answers
1k views
+200

What does B3LYP do well? What does it do badly?

I have seen a general criticism of B3LYP in computational chemistry (especially with the 6-31G* basis set). I would like to know some of the more/less obvious problems that occur when using it and ...
6
votes
0answers
39 views

Why does the Fermi energy change when doing NSCF at different nbnd values?

While doing NSCF, I decided to rerun it at higher nbnd values to incorporated more unoccupied states while plotting PDOS. But the Fermi energy gets changed with ...
11
votes
2answers
324 views

What is the difference between DOS and PDOS?

I'm new to DFT. Can you please help me to understand DOS and PDOS (projected density of states) in simple wording? I only want to know some basics of these terms and how they are linked to DFT.
6
votes
0answers
38 views

Band unfolding for magnetic systems

I'm trying to study the electronic structure of a 1D antiferromagnetic (in which the spin is associated with copper atoms) via spin-polarized calculations. The unit cell dimensions are provided below (...
9
votes
1answer
190 views

How to calculate the band structure of a protein molecule

I want to calculate the band structure of a protein molecule. How can I do it using Siesta of Gaussian? I am thinking about QE/VASP as the number of atoms are 600 and computationally it is not ...
5
votes
1answer
25 views

How to interpret the affinity in a protein docking - ligand

I'm performing a molecular docking using a trans-membrane protein and several ligands. For the first ligand, the best conformation gave a binding energy of 110 kcal/mole, being 50 kcal/mole the ...
9
votes
1answer
52 views

Excluding certain sp3-hybridized carbons with SMARTS

Let's say I have a compound shown above (SMILES: CCC(F)(F)F), and I want to exclude the trifluoromethyl group with SMARTS, how would I do that? I have tried ...
9
votes
1answer
65 views

Why VASP calculates the elastic constant for another trigonal space group?

Please, help me to understand the problem. I calculated the elastic constants for the beta PHB (Space group P3221 (154)), it has to show the reduced elastic constant matrix (six), however, ...
11
votes
1answer
46 views

What does this temperature & total free energy profile mean (obtained from VASP NVT molecular dynamics simulations)?

In order to obtain molecular dynamics (MD) simulations trajectory for computing phonon dispersion relation at finite temperature, I performed NVT MD simulation using VASP for my target system. Here is ...
5
votes
0answers
25 views

Construct a parity operator in TRIM

I want to calculate the band parity at some TRIM in Brillouin zone. Parity was defined as the eigenvalue of the inversion operator. My question is how to construct the matrix representation of the ...
4
votes
0answers
16 views

Can we calculate the intermembrane protonation state?

I want to know the protonation state of the intermembrane subunit of a protein. For that, I need to know the pH, so given that small molecules can cross the lipid bilayer, could we assume intracelular ...
6
votes
4answers
666 views

How to create a lookup table of ϵ and σ values for Lennard-Jones Potentials?

So in my last question How may I calculate the bond length between two atoms? I mentioned that I want to use Lennard-Jones Potential to simulate atom/molecule interaction for my sandbox-game-like ...
8
votes
1answer
97 views

Chimera or other software to perform protonation states of a protein

I want to perform a Molecular Docking between some ligands and a protein in different pH conditions. For this, I calculated the distance between atoms in different pH concentrations for the ligands, ...
6
votes
1answer
42 views

problem using GPAW in Google Colab

I am trying to follow the following: https://peterschindler.github.io/ This is searchable on the internet and it shows how to use GPAW as an ASE calculator. The installation is done by ...
10
votes
2answers
78 views

How to create a differential spectrum from two simulated spectra, calculated by two different basis sets?

In my bachelor thesis, I compare simulated IR-spectra computed by different basis sets. The simulated spectra from sets like cc-pVTZ and cc-pVQZ are too similar to compare them by plotting them next ...
6
votes
1answer
26 views

How to go from tinker parameters to a GROMACS itp file, specifically for dihedrals?

I am trying to write an itp file for the compound 1,2-diethoxyethance (CCOCCOCC).I used tinker analyze to obtain the parameter file, f2.out, which I have attached to this post. In order to check if my ...
11
votes
6answers
746 views

How may I calculate the bond length between two atoms?

I have been looking into Lennard-Jones Potential and Morse potential. And what the formulas do is to calculate a potential and the 'well depth' and 'distance at which the intermolecular potential ...
4
votes
1answer
44 views

Optical anisotropy from first-principles

I am interested in the theoretical study of optical anisotropy (birefringence, dichroism etc.) of different materials. I have seen DFT works studying optical anisotropy from the calculation of ...
15
votes
6answers
2k views

How do I simulate the interaction between two atoms?

I want to build a rough atom interaction simulator, where pushes two (or more) atoms toward each other and they should behave physically correctly: attract, bond or repel with some force. So that is ...
7
votes
1answer
36 views

How to determine the more stable configuration between a flat and a buckled monolayer with DFT?

Using first principles methods (quantum espresso code) I would like to find if a monolayer of a material is flat or buckled. Using the van der Waals interaction in the calculation I found that the ...
7
votes
1answer
81 views

Avogadro for Linux — Input Generators and Submitting Job to QM software?

Regarding input generators for a Linux (Linux Mint 20.1 Xfce) version of Avogadro2, I have managed to get this working using the Flatpak version and copying the input generator python scripts from ...
7
votes
1answer
167 views

Problem obtaining a Raman spectra of a graphene structure

I am trying to obtain the Raman spectra of a graphene structure using Gaussian. I used the input below, but when I did it, I got this error: ...
6
votes
1answer
38 views

How to make this DOS plot more smooth and add more points around Fermi level?

I have calculated and plotted the DOS for a doped monolayer 3x3x1 supercell. I want to make the plot more smooth and add more points around Fermi level. Knowing that these are my settings for the ...
4
votes
1answer
55 views

Has there been any work done on fluid dynamic or acoustic modeling of the human oral (or nasal) cavity?

The purpose is for me to develop a deeper understanding of speech production and how distinct features that identify a phenome are produced. ab initio models based on classical & statistical ...
4
votes
0answers
31 views

If a molecule's theoretical formation energy is positive, can it still be synthesized?

I have designed a molecule using hydrocarbons A and B. I am getting the formation energy slightly positive (~0.04 eV). As per my experience, any positive formation energy means that the designed ...
7
votes
1answer
36 views

How to go from Tinker parameter file to GROMACS topology file for improper and proper dihedrals?

I have been playing with a polymer called glyme, and I have run Tinker analyze on it to get OPLS-AA parameters for it. I have attached the output parameter file to this post. My question is, how do I ...
5
votes
1answer
41 views

Is it possible to analytically solve for a particular phase region of a CALPHAD database? (instead of guessing and checking)

As I understand it, a given CALPHAD database is essentially just a set of equations that model the Gibbs free energy of each phase within a given alloy system (set of elements). Typically, the main ...
3
votes
1answer
19 views

Procedure to validate glide docking without a reference ligand on Autodock vina

How can I perform a score-in-place procedure with autodock to validate ma glide docking? It is a new software for me and I don't Know how to use it and how to proceed. Thanks in advance for help.
8
votes
1answer
39 views

When import volumetric data (spin density of CHGCAR) to VESTA which option should we pick here?

I am trying to plot SPIN DENSITY isosurfaces using VESTA. I have used vaspkit option 312 to create ...
7
votes
1answer
37 views

Read a data file into the atoms object in ASE

There isn't that many tutorials on Atomic Simulation Environment on the net and among those I saw, the atoms object is always built explicitly within Python. What if I have a data file containing the ...
11
votes
3answers
1k views

How to make a python code that can read a .xyz file and find the distance between atoms?

I want to make a python script that will load an xyz file. From the xyz parameters, I need to find the distance between atoms, angle and dihedral between atoms. The file xyz have this structure: ...
7
votes
2answers
71 views

How to use gnuplot to draw Bandstructure and DOS from VASP outputs?

I am wondering if you could show me how to use gnuplot to draw bandstructure and DOS plots starting from VASP outputs. If you have any scripts please share them with us. Thanks.
5
votes
1answer
50 views

Docking validation RMSD over 3, How can I fix it?

I performed a molecular docking and when I tried to validate it, the RMSD values are over $3 \overset{\circ}{\mathrm{A}}$. I don't understand how I can fix it. Could someone help me? Thanks in advance....
6
votes
1answer
89 views

How can I validate docking result without a co-crystallized ligand?

I have to validate one of my docking protocol but I haven't a co-crystalized ligand. There is a way to validate it? Thanks in advance.
5
votes
1answer
48 views

What are the more efficient, or easier, methods of handling electromagnetic interactions?

Since metals, metalloids, non-metals, and composites, have differing characteristics, plug-and-play methods, so to speak, would be useful. Also, as it’s well known that a moving electrical field ...

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