All Questions

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.

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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: ...

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\...

I've tried to calculate dispersion energies of some organometallic complexes with the Gaussian software using WB97XD/Gen (...

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 ...

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 ...

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 ...

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 ...

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 ...

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.

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 (...

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 ...

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 ...

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 ...

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, ...

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 ...

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 ...

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 ...

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 ...

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, ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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: ...

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 ...

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 ...

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 ...

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 ...

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 ...

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.

I am trying to plot SPIN DENSITY isosurfaces using VESTA. I have used vaspkit option 312 to create ...

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 ...

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: ...

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.

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....

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.

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 ...