Questions tagged [charged-molecules]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
2 votes
2 answers

How to select charge and multiplicity for macro-molecules?

In optimising proteins with DFT/B3LYP, how can we detect the charge and multiplicity of the protein?
PriZarah's user avatar
  • 301
5 votes
1 answer

Valence correction by adding formal charge in RDKit

I am modeling molecules as graphs, with nodes as atom types and edges as bond types (single, double, triple). I do not model formal charges or hydrogens explicitly (only heavy atoms). When trying to ...
Njw96's user avatar
  • 191
3 votes
2 answers

How to merge two files (molecule structure and file property) into one?

I've run some calculations with the xtb software. From its output I got XYZ and MOL files ...
Camps's user avatar
  • 22.3k
9 votes
1 answer

Simulation of charged species with plane-waves in Quantum Espresso

I am using Quantum Espresso to simulate a platinum surface with ligands, so far everything is working ok. I now need to introduce a solvated hydronium $\ce{H_3O^+(H_2O)_2}$. Is there something I ...
Okano's user avatar
  • 1,222
9 votes
1 answer

What is a "charged system" in this specific context?

I'm doing a polarization calculation for the first time. To specify one of the input parameters (the "reference point") correctly, I have to figure out if my system is "charged." ...
NTS's user avatar
  • 719
9 votes
1 answer

Generating topology for charged molecules

I have to generate a topology file for a molecule like Sodium Triphosphate, and I do not find forcefields available in the literature. So as a starting point would like to use engines like LigParGen ...
Kavya Mrudula's user avatar