Questions tagged [computational-chemistry]
For questions about computational chemistry.
38
questions
6
votes
1answer
45 views
Which basis set should be used for a system that contains both anions and cations?
I am trying to model a system that has both anions and cations interacting with each other. (In this case it is calcium ion interacting with two small carboxylic acid molecules). Now, looking through ...
10
votes
0answers
41 views
+50
Bioisosteric replacement using SMARTS (KNIME and RDKit)
I am trying to create a KNIME workflow that would accept a list of compounds and carry out bioisosteric replacements (we will use the following example here: carboxylic acid to tetrazole) ...
15
votes
2answers
43 views
What is the difference between orbital localisation and NBO?
I am new to computational chemistry, I have used mainly GAMESS and Orca. In GAMESS, there are orbital localisation schemes like Pipek-Mezey, Ruedenberg-Edminston, etc. which generate orbitals that ...
10
votes
2answers
97 views
How to get potential energy surface from GAMESS?
I'm trying to learn GAMESS and performing a simple PES scan of oxygen molecule. After the completion of the calculations I get a .log file with lots of sections like that:
...
7
votes
0answers
59 views
What is the physical meaning of occupations='smearing' in Quantum ESPRESSO?
I want to understand, what is the intuition behind using the occupations='smearing' or 'tetrahedra' in Quantum ESPRESSO input file? I mean how we can interpret what is going to happen inside of ...
8
votes
1answer
66 views
How to do spin polarization calculations using Quantum ESPRESSO?
I am currently new to DFT calculations in Quantum ESPRESSO. Though, I have read some research papers for determining spin polarization and Half-metallicity in certain Heusler alloys. These research ...
10
votes
1answer
108 views
Predicting magnetic moment of a metal complex computationally
Recently, for entrance exams, I have been dealing with a lot of weird compounds. One of them is $\ce{K3[Mn(CN)6]}$.
The objective was to predict the magnetic moment of the above complex.
I predict ...
9
votes
2answers
147 views
How to choose pseudopotential for DFT calculations in Quantum ESPRESSO?
I am a beginner and newly started running DFT calculations to find out the electronic band structure of certain materials in Quantum ESPRESSO. But we have to select the pseudopotential for running the ...
8
votes
0answers
61 views
VASP's NPAR and KPAR for parallelization
What's the best way for parallelization in VASP for periodic systems? In the documentation, it mostly explains it for the local computer and molecule calculation. Apparently, these explanations don't ...
9
votes
1answer
341 views
High precision helium energy
In the paper "High Precision Theory of Atomic Helium", Drake lists the then best-known ground state energy of the Schrödinger equation for helium to 22 digits as:
$$\lambda_0 \approx -2....
9
votes
1answer
40 views
How can I determine the maximum value of a spin orbital and its derivative in any direction?
I'd like to be able to recover the maximum value that any of the basis functions can take, as well as their maximum derivative. How can I do this?
For context, I need it because I want to calculate ...
9
votes
2answers
51 views
Analytic Hessians for meta-GGA functionals
In many of the free/open-source QM programs like GAMESS, ORCA, NWChem, the calculation of analytic hessians is not possible when a meta-GGA density functional is used, like M06-2X. My first question ...
8
votes
1answer
103 views
Are there other custom chemistry programming languages besides SVL?
I must confess some ignorance... I just became aware of the Scientific Vector Language (SVL) which has been around since 1994 and was created solely for computational chemistry.
It has a large ...
9
votes
0answers
62 views
Correcting thermodynamic data for concentration, what concentration is best to use?
In computational chemistry when using transition state theory we often use standard states for all involved structures. However, sometimes people argue that it should be corrected for concentration (...
18
votes
2answers
698 views
Why do people care about reversibility in molecular dynamics simulations?
When carrying out a molecular dynamics simulation, one has to choose an ensemble. Depending on the problem, one usually works in the microcanonical (NVE), canonical (NVT), or grand canonical ensemble (...
8
votes
0answers
59 views
Equilibration of normal modes in water molecule [closed]
When running a molecular dynamics simulation on a singular water molecule in vacuum to analyze its normal modes of vibration from the NVE (microcanonical) ensemble, the bending mode frequency is ...
8
votes
1answer
103 views
How to perform virtual crystal approximation calculations in VASP?
Can someone share appropriate tags and methods to perform virtual crystal approximation calculations in VASP?
8
votes
1answer
111 views
How to fix Error Link9999 in Gaussian
I have a problem with geometry optimization in Gaussian software with M062X method. The structure was smoothly optimized using M062X/Gen. Nevertheless, I need very accurate results so afterwards the ...
9
votes
1answer
115 views
Semi-canonicalisation vs canonicalisation of the Fock matrix and orbitals
I have seen the terms semi-canonicalized and canonicalized used in relation to the Fock matrix, density matrices, and orbitals; however, I am unsure what these terms actually describe.
For instance:
...
7
votes
0answers
40 views
What are the methods of modeling Jahn-Teller effects in a solid-state material?
The Jahn-Teller effect arises from the symmetry breaking (distortion) of the local environment for the crystal field of 3d transitional metal ions.The distortion result in energy saving of electronic ...
6
votes
1answer
69 views
I get an error 'Conversion from Z-matrix to cartesian coordinates failed' in Gaussian09. Any suggestions?
I'm doing my calculations using G09W. My OS is Windows 7 (64-bit). This error occurs in the frequency calculation. What's even weirder is that it seems to happen right after everything is already ...
6
votes
1answer
37 views
I get this error in Gaussian09 even though I have enough memory. “Error termination in NtrErr: NtrErr called from FIOCnC.” Any suggestions?
Whenever read-write files get to about 20Gb, I get this error. I know that, in G09, one rw file is limited to 16Gb. So I have set the software to write several RWFs. But it still keeps producing this ...
14
votes
3answers
414 views
How well can we model chemical synthesis?
The Materials Genome Initiative held a 2017 workshop, that led to this published report: de Pablo et al., "New frontiers for the materials initiative," npj Computational Materials 5, 41 (...
13
votes
4answers
150 views
What is the role of a chemist in computational chemistry?
As someone that wants to learn about computational chemistry, mainly for its use in energy storage materials (and therefore DFT as the most practical method of it), I am wondering what is essential ...
12
votes
1answer
88 views
Calculate spin-spin coupling based on previous GIAO calculation with Gaussian
I used GAUSSIAN/GAUSSVIEW to calculate the GIAO Magnetic shielding tensor (ppm), but I forgot to calculate the Nuclear spin-spin coupling J (Hz). How can I use the .chk file or .log file to calculate ...
14
votes
1answer
213 views
How can I scan the whole PES of a bulk structure?
I am not very familiar with scanning a PES for a bulk structure, and I'd be very appreciative for some suggestions.
13
votes
2answers
129 views
A CCSD(T) geometry optimization in Gaussian09 is deviating too far from the minimum. How do I deal with it?
I am doing a CCSD(T) geometry optimization on a series of molecules. One of the geometry optimizations took about 2 weeks even though an analogous molecule with the same number of basis functions took ...
16
votes
6answers
270 views
What are the applications of chemical graph theory?
Graph theory was originally introduced in computer science to study data structure. Chemists also introduced graph theory to study the relation between structure and properties for molecular compounds....
8
votes
1answer
99 views
The correlation energy from frozen natural orbtials (FNOs) using CCSD and MPBT(2)?
In other works and from the paper: Scaling Up Electronic Structure Calculations on Quantum Computers: The Frozen Natural Orbital Based Method of Increments.
I have seen that the corrected CCSD ...
11
votes
2answers
209 views
One-center two-electron integrals between 1s STO
As per @user1271772 's suggestion I am asking this question here again.
I am trying to understand SCF cycle by trying to code up solved example from Quantum Chemistry by Levine (page 443, 5th edition)...
14
votes
1answer
126 views
How the projected density of states is built
I'm new to DFT. I'm trying to figure out how projected density of states (PDOS) is built in solid state physics software package.
I understand the basics of the density functional theory method: each ...
12
votes
1answer
81 views
What is the impact of the orientation of a molecule in cartesian coordinates to molecular properties?
According to my knowledge, each computational chemistry code optimizes a molecule keeping the input orientation of the molecule. The population and spectral analysis is performed on the optimized ...
9
votes
0answers
74 views
Is there any literature that systematically analyzes current quantum chemistry algorithms using Big O notation for time and memory cost? [closed]
Big O notation is commonly seen in the papers on novel computational methods. However, only a few of them include rigorous analysis of the algorithm. Is there any literature that summarizes current ...
24
votes
2answers
2k views
What are the “smart algorithms” applied to solve the “curse of dimensionality”?
The "curse of dimensionality" is an ubiquitous issue arising in both electronic structure and quantum molecular dynamics, which refers to the exponential scaling of computational cost with ...
15
votes
1answer
207 views
CCSD(T) Transition State and Ground State Calculations in Gaussian09: “Unable to Determine Lambda”?
I’m doing CCSD(T) calculations (for both transition and ground state geometries) on a series of small molecules in Gaussian09. Several similar calculations terminated without any problems but one TS ...
8
votes
1answer
64 views
What chemical systems can be modelled without the use of approximations? [closed]
Because of its size, for example a protein can not be modelled from the quantum chemical basis in a reasonable amount ot time without approximations. A hydrogen atom though can, manually even.
Where ...
19
votes
3answers
233 views
What software is needed in chemoinformatics or materials modeling, that a solo programmer could work on?
I want to make a pet project in cheminformatics and I need to hear from the community about the actual challenges in chemistry that might be resolved with a digital solution.
I've been working in ...
25
votes
1answer
294 views
Approximate equivalence table between Pople's basis sets and Jensen's DFT optimized polarization consistent basis sets (pcseg-n)
At first I posted this question in chemistry.stackexchange.com, before materials.stackexchange.com was launched in beta. As it went unaswered, I'm giving a try here.
I have some calculations results ...
