S R Maiti
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3 answers
23 votes
1k views
Geometry optimization: what happens in the algorithm?
17 votes

To add to the other answer, the energy of a molecule (or any chemical species) can be expressed as a function of the coordinates of the atoms. Most softwares convert the 3N cartesian coordinates into ...

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3 answers
13 votes
569 views
Script to generate input files for benchmark purpose
12 votes

This is an alternative approach with Python scripting. For bash scripting, @NikeDattani has already posted an excellent answer. Let's say you are trying to run the input files with GAMESS. Start with ...

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1 answers
13 votes
249 views
How to calculate and plot localised orbitals with xTB?
11 votes

You can do it with Multiwfn (http://sobereva.com/multiwfn/) First, xTB has to be run with the --molden directive, to output the converged molecular orbitals as a molden file. Normally xTB will produce ...

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2 answers
15 votes
288 views
What's the best quantum chemistry output parser for the command line?
10 votes

CCLIB Cclib is an open source python library that can parse and interpret output files of common computational chemistry programs. As of now, it supports Psi4 version 1.0 and 1.2.1. It can be called ...

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2 answers
12 votes
329 views
For DFT and Hartree-Fock, how can we know that we have a true minimum? Is there an equivalent to the "frequency analysis" for geometry optimization?
10 votes

Just like geometry optimization, there is no practical way to be 100% sure that you have the global minimum of SCF solutions. But there are checks you can do to make sure that the SCF solution you got ...

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1 answers
12 votes
158 views
Functional group detection from geometry
Accepted answer
10 votes

You can probably do it with only OpenBabel or RDKit using SMARTS search strings, but you can get a much easier solution if you combine OpenBabel with checkmol (which you have mentioned in the question)...

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2 answers
14 votes
200 views
Finding parameters for a molecule in various forcefields
Accepted answer
8 votes

Running simulations with small molecules is one thing that I found quite difficult especially because most online guides/tutorials are focused on proteins. So, here's a rough idea of what to do: ...

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5 answers
32 votes
3k views
What is a good replacement for Gaussian?
8 votes

NWChem Official website: https://nwchemgit.github.io/ and https://www.nwchem-sw.org/ It is open source Description: NWChem aims to provide its users with computational chemistry tools that are ...

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1 answers
9 votes
194 views
Mismatched number of normal modes calculation in GAMESS
Accepted answer
8 votes

Firstly, a minor correction: a non-linear molecule has 3N-6 normal modes, not 3N-5 modes. Linear molecules have 3N-5 normal modes. GAMESS automatically prints out some values in normal coordinate ...

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2 answers
6 votes
445 views
Analytic Hessian at the level of full CI?
Accepted answer
6 votes

GAMESS also should be able to calculate analytic hessian for the full CI case. From the GAMESS manual: $FORCE group (optional, relevant for RUNTYP=HESSIAN,OPTIMIZE,SADPOINT) This group controls the ...

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1 answers
5 votes
428 views
Error in GROMACS for adding ions to a solution
6 votes

As I had previously written in the comments, the warning given by gromacs seems to indicate that the GROMOS force fields should not be used due to wrong parameterization: The GROMOS force fields ...

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2 answers
8 votes
288 views
Is the number of basis functions same in the different atoms in the 6-31G basis set?
6 votes

I think that it is a feature of how the basis set is defined. 6-31G is a valence double-zeta basis set of the Pople family. Here, 6 means that the core orbitals are represented with 6 Gaussian ...

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2 answers
9 votes
218 views
How do you generate 3D electron density from fchk file without the Gaussian software?
6 votes

The other answers have already covered how to generate the formatted checkpoint file (.fchk). So in my answer I will attempt to explain how to use Multiwfn to get the electron densities from the .fchk ...

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6 answers
12 votes
1k views
How may I calculate the bond length between two atoms?
6 votes

I don't know why you need atom-atom interactions in a sandbox game. My only guess is that you want to simulate or visualize the movement of molecules of some kind in real time. If your system is large ...

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1 answers
7 votes
59 views
PES of Tetramethylthiuramdisulfid / Problem with Disulfidbridge
Accepted answer
6 votes

Without seeing the result of the scan, my guess would be that it is a visualization problem with gaussview, and it has nothing to do with the calculation. Gaussview detects bonds by the distance ...

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1 answers
8 votes
107 views
Optimization and vibrational analysis of excited state CO using GAMESS
Accepted answer
6 votes

I cannot see your output file, but I am pretty sure that the program is running into an error when starting the optimization i.e. when it is trying to generate the guess hessian. You are using ...

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2 answers
6 votes
194 views
Excited state normal mode frequency doesn't match for NH3
Accepted answer
5 votes

This is not a full answer, because it does not solve the problem. But I hope to shed some light on why you are not getting the correct frequencies. Short answer: I suspect there is a bug in GAMESS ...

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1 answers
10 votes
144 views
Computing optimized 3D structures in python that take solvent into account
Accepted answer
5 votes

From reading your comments, and the question, you want to generate optimized structures of small bioactive molecules in solvents, but it has to be fast. I would definitely recommend using semi-...

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9 answers
29 votes
784 views
Is there a free package with robust CASSCF functionality?
5 votes

GAMESS GAMESS (https://www.msg.chem.iastate.edu/GAMESS/) has an MCSCF module, which can perform CASSCF. For generating configurations it can use determinants, or configuration state functions (CSFs). ...

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12 answers
16 votes
8k views
Is it better for me to study chemistry or physics?
5 votes

I was in the same position as you 3 years ago! I liked chemistry the most and physics the second, but my dad is a physicist so he wanted me to study physics. I ended up choosing chemistry because math ...

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2 answers
8 votes
482 views
Why can MD simulations not handle "exotic" materials?
4 votes

By molecular dynamics, I assume you mean molecular dynamics using force-fields (a.k.a. Classical Molecular Dynamics). Remember that there is also ab initio MD. Force fields are parameterised, i.e. ...

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2 answers
9 votes
110 views
Is it possible to do a Gaussian redundant scan with some fixed bonds?
Accepted answer
4 votes

I think @romaichenko's answer covers everything. But for a full answer I believe a sample input file is necessary. # B3LYP/6-31G(d) Opt=ModRedundant methane with H 0 2 C -1.41531 0....

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1 answers
5 votes
60 views
Have I missed something? RDF (radial distribution) script cannot capture the correct .xyz
3 votes

Ok, I think I figured out why your code is giving a straight line. This is too big to write as a comment, so I am putting this as answer. At the start of the function, you are determining the edges of ...

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2 answers
12 votes
129 views
Avoiding charge-migration in electronic structure calculations with solvent-like environments
3 votes

I am not too experienced on this topic, so take my answer with a grain of salt. PCM (Polarizable Continuum Model) deals with solvation effects by assuming that the effect of solvent molecules ...

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4 answers
9 votes
275 views
What programs can do electron integrals and SCF calculations with more than one CPU?
2 votes

GAMESS Most parts of GAMESS are parallelised with MPI (including SCF), and can run on multiple CPUs. The parallel SCF runs entirely on replicated memory, however other parallel algorithms such as MP2, ...

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