14
votes
Accepted
How to export a calculated Raman spectrum in Q-Chem, as a Gaussian profile?
I wrote the following simple Python function that allows one to use any distribution from scipy.stats for peak broadening (the ...
- 1,700
13
votes
How to calculate DFT energy with density from another level of theory?
Incidentally, I initiated some discussions along these lines in these questions for HF-DFT (also called 'density-corrected' DFT) here,
and here. I'm familiar with Quantum ESPRESSO, so I can detail a ...
- 2,426
13
votes
What is the most user friendly software for frequency visualization rendering?
VMD Normal Mode Wizard
If you're goal is to create high quality visualizations of vibrations I recommend VMD. It's highly customizable in terms of colors, resolution, and representation.
The setup ...
- 7,957
12
votes
What significant matter modelling methods are implemented in commercial software, for which there is no freeware alternative?
I think the way this question is asked is a little too simplistic. In order to execute a computational project, there is always more than one calculation required. Even if you are happy with the ...
- 274
11
votes
How to export a calculated Raman spectrum in Q-Chem, as a Gaussian profile?
Many thanks to Felipe, the code is very useful! I know this is just a simple editing, but this is how I adjusted part of the code for Raman spectra:
...
- 1,658
11
votes
Accepted
How to calculate homolytic bond dissociation energies?
Multi-reference or single-reference?
While it is appreciated that near dissociation there will be a near-degeneracy of orbitals, requiring a multi-reference treatment, fortunately we don't have to ...
- 33.7k
9
votes
Why is Q-Chem producing a parallel efficiency greater than 1?
While I am not completely familiar with all the details in Q-Chem's SCFs, I am aware that there are in fact multiple SCF implementations and multiple implementations for computing two-electron ...
- 2,384
9
votes
What is the most user friendly software for frequency visualization rendering?
Jmol
The Jmol package is able to do what you want. You can produce the animations below just using point & click with your mouse.
But you can also use its scripting capabilities to work with batch ...
- 22.4k
9
votes
How is "basis set projection" done?
What you're describing is very common, and is not limited to GAMESS and Q-Chem.
First, here's how to do it in MOLPRO, MRCC, GAMESS, Q-Chem (in fact the only electronic structure software that I ...
- 33.7k
8
votes
Accepted
How is "basis set projection" done?
Supplementing Nike's answer above.. This is actually quite elementary math. Let's say I have an orbital in a basis
$|\psi\rangle = \sum_i c_i |i\rangle$ and I want to find the expansion in some other ...
- 18k
8
votes
How to calculate homolytic bond dissociation energies?
BDEs are calculated by the below procedure:
Calculate initial energy
Perform homolytic bond cleavage and separate fragments
Calculate energies of the fragments, add the energies together
Calculate ...
- 1,526
8
votes
Which SCF energy to use to plot PES after calculations with SMD?
Generally you want to use the same settings when trying to combine results from different jobs. However, below is the general procedure that I have seen performed for a basic, publishable PES.
1) ...
- 1,526
8
votes
Accepted
Why is Q-Chem producing a parallel efficiency greater than 1?
Yes, this is correct explanation. There are three SCF codes and two integral libraries and which ones are executed depends on the job parameters (single core, multicore, multi-node). If accurate ...
- 274
8
votes
What significant matter modelling methods are implemented in commercial software, for which there is no freeware alternative?
One can also pose the opposite question, which may be more interesting: what significant matter modelling methods are implemented in open source software, for which there is no commercial alternative? ...
- 18k
7
votes
Accepted
TS-search with explicit solvent
Explicit solvent can be of importance, like you mention, whenever strong coordination or hydrogen bonding is involved. For example, transition metals often coordinate to solvent and not including them ...
- 7,957
7
votes
Is there a software that can calculate collision cross-sections involving molecules with several atoms?
iMos
iMos is Ion Mobility Software based on MATLAB parallelized code that can model Collisional Cross-Section. Tool is available for macOS, Linux and Windows and developed by Carlos Larriba-Andaluz. ...
- 1,658
6
votes
How to calculate homolytic bond dissociation energies?
One thing the other answers haven't mentioned is the zero point and thermal corrections to the BDE.
As mentioned in the Wikipedia Morse potential article, a geometry optimization will take you, by ...
- 9,045
6
votes
Parse linked frequency calculations with cclib
I think the easiest way to parse multiple-job files from Q-Chem is if you just manually split the output file into the parts that pertain to the individual jobs. Just locate where the first job ends ...
- 1,431
5
votes
How is "basis set projection" done?
Note: I have corrected some omissions from my initial answer to avoid any confusion. For a rigorous explanation of the process, I would recommend looking at Susi's answer.
The projection process for ...
- 15.2k
4
votes
Accepted
How to calculate DFT energy with density from another level of theory?
So this question is related to the recent discussion in Procedure to classify errors in Kohn-Sham DFT where I already gave the general procedure: get the density from some level of theory, and use it ...
- 18k
4
votes
How to set up a local server for iQmol on macOS?
I do not think the server setup is the problem per se. By default, IQmol is setup to submit jobs to a server that is owned by Q-Chem and those jobs are time-limited at 5-10 min. (The precise limit ...
- 49
4
votes
Accepted
When running DFT on Q-Chem with an HPC cluster, why is parallelization with OpenMP faster than with MPI?
I am not at all surprised that using 16 cores on one node with OpenMP is faster than using 16 cores spread across 4 different computers (nodes). The 16 cores on a single node are usually part of the ...
- 33.7k
3
votes
Q-Chem QM/MM options
The Q-Chem manual edition 5.2 is much better at describing QM/MM
However, to answer your main question there are no angles and torsions across a link atom. The link atom is a fictitious hydrogen that ...
- 7,957
2
votes
Which SCF energy to use to plot PES after calculations with SMD?
I really don't know the output structure of Q-Chem, but in SIESTA, we have the following information:
...
- 22.4k
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