Community Digest

Top new questions this week:

Considerations when developing ab initio based interatomic potentials for classical molecular dynamics

I know that there are published interatomic potentials provided for most elements when using classical molecular dynamics tools such as LAMMPS. However, if someone were to use their own DFT ...

density-functional-theory lammps interatomic-potentials  
asked by PBH 8 votes
answered by B. Kelly 6 votes

Why don't we use the principal quantum number when building the projected density of state?

I am using VASP to calculate the projected DOS, but I am not sure why we aren't using the principal quantum number when doing the projection. According to the VASP wiki, LORBIT would control VASP to ...

density-functional-theory vasp density-of-states  
asked by Jack 6 votes
answered by Tristan Maxson 6 votes

How to predict protonation state of molecules in water?

I'm interested in predicting the protonation and tautomer state of organic molecules (typically CHNOS) at near pH 7 in water. I've used tools like Schrodinger's Epik / LigPrep before, but they ...

software quantum-chemistry  
asked by Alex I 6 votes
answered by Geoff Hutchison 6 votes

How could I fold a specific high symmetry point to the Gamma point?

How could I get the Brillouin Zone of 2*2 supercell? I tried to use see k-path website, but when I upload a supercell, it still generates the Brillouin Zone of the unit cell. What I want to do is to ...

k-points brillouin-zone supercell  
asked by Jack 6 votes
answered by ProfM 5 votes

Fermi energy lower than valence band maximum?

I am trying to analyze the density of electronic states of a $\ce{TiO2}$ slab, but the result I got from VASP shows the fermi energy is lower than the valence band maximum (VBM) by a small energy ...

density-functional-theory vasp fermi-energy semiconductor  
asked by Jack 5 votes
answered by Phil Hasnip 5 votes

How to add a bond between two atoms in VMD?

I want to add a bond between specific atoms. I found on VMD page that one can use topotools (e.g. topo addbond 1 2 ), but I have a lot of residues so this method ...

visualization-software vmd  
asked by Abd-Elazeem Mohamed 5 votes
answered by Vasista 3 votes

Calculated Redoxpotential is too far away from experimental value

I calculated the redox potential with Gaussian for hydroquinone with different combinations of functional/basis sets always values like 5.4V (B3LYP/6-311G+(2d,p) and SMD model). The experimental value ...

density-functional-theory gaussian redox  
asked by Andrea 5 votes

Greatest hits from previous weeks:

DeepMind just announced a breakthrough in protein folding, what are the consequences?

There was some recent media reporting about a purported Google breakthrough on applying machine learning techniques to tackle the protein folding problem, as told for example in this news article, ...

molecular-modeling proteins machine-learning structural-biology protein-folding  
asked by ksousa 53 votes
answered by Nike Dattani 56 votes

Should I connect 2-3 laptops to form a supercomputer?

I have recently started to use Quantum ESPRESSO for evaluating different properties of ZnSe Quantum Dots. But I currently don't have access to any cluster and as I am increasing the size of ...

quantum-espresso high-performance-computing windows-operating-system  
asked by Parmeet Singh EP 066 14 votes
answered by Nike Dattani 17 votes

Given the adjacency matrix of a molecule, how can I get a graphical representation using only open source software?

In Huckel Method, by numbering the sp2 carbons in a molecule with conjugated double bonds, we can assemble its secular determinant in a form similar to the adjacency matrix of a graph. Taking trans-...

molecular-modeling software-recommendations mathematical-modeling open-source cheminformatics  
asked by ksousa 8 votes
answered by dwhswenson 9 votes

When should spin polarized calculations be done?

Should the presence of a d block element in the unit cell mandate the need for performing spin-polarized calculations? I wanted to find out the DOS, PDOS, and the band structure. I'm new to DFT and I'...

density-functional-theory vasp quantum-espresso magnetism spin  
asked by Anoop A Nair 11 votes
answered by Thomas 8 votes

How to choose starting magnetization while doing spin polarised calculation in Quantum ESPRESSO?

I am trying to run spin polarised DFT calculation in Quantum ESPRESSO on system Co2MnSi. I kept starting magnetization for all these three species as, ...

density-functional-theory quantum-espresso computational-chemistry spin-models spin-polarization  
asked by UJM 6 votes
answered by Jack 4 votes

How to carry out HSE06+SOC band structure calculation using VASP?

I could not find any good source for this type of calculation. I'd be very appreciated if someone who is experienced with that to show it step by step

density-functional-theory vasp hse06  
asked by Savir 9 votes
answered by Jack 11 votes

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 ...

density-functional-theory computational-chemistry surfaces functional catalysis  
asked by Tristan Maxson 25 votes
answered by Tyberius 17 votes

Can you answer these questions?

How to get the right type of bandgap(indirect/direct) in VASP?

I am trying to calculate the band gap type(Direct or Indirect) of TiO2-Rutile, according to the Material Project, rutile is a direct bandgap type semiconductor. The VBM and CBM are both at the Gamma ...

vasp electronic-structure bandgap  
asked by Jack 4 votes

Database of surface electronic structure

I'd like to compare my simulation result of a TiO2-110 surface's electronic structure, but all the literature shows too many different results, so I'd like to look for a database for surface ...

density-functional-theory electronic-structure surfaces databases transition-metals  
asked by Jack 1 vote

Translate INCAR to Python script using ASE

I am considering using ASE to translate my old work into a Python script. I already have the INCAR and POSCAR KPOINTS files. Is it possible to let ASE read these files and generate Python scripts that ...

vasp software atomic-simulation-environment  
asked by Jack 3 votes
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