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Special tag for certain big-list questions. Answers should only go into detail about one specific topic related to the question. The original question will often present a template format for submitting answers.

13 votes
4 answers
4k views

Molecular visualization software in Jupyter (IPython) Notebooks

Jupyter notebooks have always been a great way for me to create high-quality graphs, and write code. The features also continue to improve with packages such as Jupyter Lab, and now Jupyter Books, whi …
15 votes

What software will allow me to combine two images?

Adobe Dimension Adobe dimension is the premier paid software for 3-dimensional design. It can read in STL files and give them a texture, and incorporate the light source from the background light. The …
Nike Dattani - No Free Time's user avatar
2 votes

What are the types of MCSCF?

DOLO (Do Localized Orbital) CASSCF CASSCF can capture static electron correlation (i.e. orbital degeneracies), and it is very important to select the active space which includes the degenerate orbital …
Cody Aldaz's user avatar
  • 8,025
14 votes

Is there a free package with robust CASSCF functionality?

BAGEL The code is available through GitHub[1] and has been described in WIRES.[2] The main advantages of BAGEL is that it has better memory and parallelization than MOLPRO. For example, MOLPRO (not F …
Nike Dattani - No Free Time's user avatar
8 votes

Candidate structures for global minimum determination

Confab OpenBabel source documentation: https://open-babel.readthedocs.io/en/latest/3DStructureGen/multipleconformers.html Example: obabel <inputfile> -O <outputfile> --confab [confab options] Some of …
Cody Aldaz's user avatar
  • 8,025
20 votes

What are the types of charge analysis?

Electrostatic potential (ESP) derived charges Note that ESP1 derived charges include ChelpG (CHarges from ELectrostatic Potentials using a Grid-based method), the Merz–Kollman (MK) 2, and the RESP (re …
Cody Aldaz's user avatar
  • 8,025
12 votes

What software is available to do molecular dynamics on Windows?

OpenMM OpenMM is a highly efficient molecular dynamics package which can run via Python. Therefore, any way you normally run python can work. For example, via a Jupyter (Ipython) notebook, via a pytho …
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