Questions tagged [charged-molecules]
The charged-molecules tag has no usage guidance.
6
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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?
- 301
5
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1
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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 ...
- 191
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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 ...
- 22.3k
9
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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 ...
- 1,222
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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." ...
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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 ...
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