Questions tagged [charged-molecules]

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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 ...
  • 19.3k
4 votes
0 answers

Localising radicals on groups or atoms in Gaussian

I am interested in computing single point interaction energy between monomers of radicals located specifically on certain groups or atoms. I have been looking at forums and so and it seems that it is ...
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 ...
  • 971
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." ...
  • 707
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 ...