Questions tagged [computational-chemistry]
For questions about computational chemistry.
63
questions
5
votes
1answer
8 views
What does “Test job not archived” mean?
I am running frequency computation with geom=connectivity in Gaussian. It all converges now but at the very end of the last convergence it says:
...
10
votes
1answer
102 views
How to generate accurate displacements along normal modes?
How can i displace my structure along a particular normal mode, without coupling to other modes ? Rather than a exact mathematical procedure, I am more interested in a software/script/package that can ...
11
votes
2answers
59 views
What is the most appropriate (and easy-to-use) all-atoms force field for liquid electrolytes?
I need to simulate a salt diluted in a liquid electrolyte. My experience is with LAMMPS, but so far I only had coarse grained toy models, and setting up the force field was straightforward. Now I have ...
6
votes
1answer
37 views
Vibrational frequency analysis for NEB result through Maestro
I have ran a Nudged Elastic Band (NEB) calculation using QuantumEspresso through Maestro to find the potential transition state. Within Maestro there is an option where you can select for NEB type ...
10
votes
1answer
101 views
Computing optimized 3D structures in python that take solvent into account
I have been using RDKit to generate 3D coordinates, cleaning-up the structures using a general-purpose force field as follows:
...
10
votes
1answer
140 views
What novel drugs are developed via CADD?
Virtual screening , protein ligand docking, MD simulation, FEP free energy calculations and the QM/MM approach have all been widely applied in optimization for drug discovery.
Which drugs that have ...
12
votes
1answer
58 views
Excited state energy gradient during geometry optimization of a target excited state
During the geometry optimization of the ground state of a molecule, we try to optimize the energy
gradient with respect to the nuclear positions such that the system remains in its lowest energy
state....
6
votes
0answers
54 views
Two-stage unbinding & binding energies with DFT
I'm trying to calculate the stability of the product of a coordinate bonding process of molecules A and B in the polarizable continuum solvent model (PCM, solvent set to water).
I'm getting energies ...
5
votes
0answers
50 views
Understanding emission spectra using TDDFT calculation
I did a TDDFT calculation to get the emission spectra of my molecule. Here are the first five roots for the emission calculation:
...
7
votes
1answer
59 views
Formation energy and Energy above convex hull as indicators of stability
I was trying to understand some indicators about the stability of materials (that basically tell you whether it can be synthesized or not.. right?).
Specifically, I'm trying to link the knowledge of ...
7
votes
1answer
33 views
The number of long-range interaction pairs in Tinker
I tested MM calculation of a benzene molecule with Tinker. The following is the xyz file used for the input.
...
13
votes
1answer
130 views
Are nuclear ab-initio methods related to materials ab-initio methods?
I just read this synopsis in Physics where scientists used first-principles nuclear physics calculations to predict the stability of 700 isotopes up to iron.
I didn't know that this was possible, ...
5
votes
0answers
67 views
What is the relation between enthalpy, ionisation potential, internal energy and HOMO/LUMO?
Is there any relation between enthalpy, ionisation potential, internal energy and HOMO/LUMO?
I am dehydrogenating a molecule and I need to study the enthalpy of dehydrogenation. If I get any relation ...
8
votes
1answer
52 views
Error running psi4 on charged molecules
I am running a simple energy calculation on a conformer of 3-Sulfopropyl methacrylate, which is given my C=C(C)C(=O)OCCCS(=O)(=O)[O-].
This is my workflow:
...
11
votes
1answer
179 views
How to get more significant digits from OpenBabel?
I am generating conformers from SMILES string using OpenBabel.
The shell script looks something like:
...
8
votes
1answer
94 views
Using OpenBabel or RDKIT Python API to generate conformers from a SMILES string
I have a bunch of monomers in the form of SMILES string and I want to generate conformers from them.
At the moment, I am using RDKit to convert these SMILES strings to .sdf files, then using ...
8
votes
2answers
251 views
How do I figure out how many monomer configurations I need for my simulation?
I am running a quantum mechanical simulation on Psi4 for a certain number of monomers to generate data for a database. Some of these monomers are short, while some are long.
At the moment, I am ...
10
votes
1answer
134 views
Calculating/Visualizing electronic density from orbital information written in the Molden format
I'm trying to obtain an electron density from orbital information written in the Molden format by the formula,
$$
\rho(\mathbf{r}) = \sum_{i}^{occ} |\phi_{i}(\mathbf{r})|^{2}. \tag{1}
$$
Is there any ...
9
votes
3answers
368 views
What is the procedure for constructing an ab initio potential energy surface for CH3Cl + Ar?
I would like to construct a model analytical potential function for collision between CH3Cl and Ar. This would be the sum of CH3Cl intramolecular + CH3Cl---Ar intermolecular potential. First I would ...
8
votes
2answers
175 views
What are Pair Natural Orbitals?
Recently, I came across electron correlation methods that use local pair natural orbitals (LPNOs) or domain-based local pair natural orbitals (DLPNO), such as DLPNO-MP2, DLPNO-CCSD etc. The dynamic ...
9
votes
1answer
82 views
Energy cut-off value for conformer calculations
I want to get familiar with the conformer calculation. I found a paper where they did the conformer calculations already for the molecule I work with. The paper can found here.
In the experimental ...
8
votes
1answer
44 views
Simulation of electronic potential from nanoparticles interacting with molecules
I work with SERS, where the Raman signal gets enhanced by the electric field of the nanoparticles. Now I like to simulate this kind of spectrum with Gaussian. I found a paper[1], where it looks very ...
11
votes
1answer
222 views
What are some of the biggest theoretical and computational challenges in Condensed Phase Chemistry?
What are some of the biggest open-questions / challenges in Condensed Phase theory and computation? What efforts are being done to answer them?
I realize Condensed Phase chemistry is a huge field, but ...
6
votes
1answer
214 views
How to choose starting magnetization while doing spin polarised calculation in Quantum ESPRESSO?
I am trying to run spin polarised DFT calculation in Quantum ESPRESSO on system Co2MnSi. I kept starting magnetization for all these three species as,
...
10
votes
1answer
112 views
What are the trade-offs setting DIRSCF to either .TRUE. or .FALSE. (the default) in GAMESS (US)?
The first software I used to run calculations was Gaussian09. When submitting a input, I used to see a pattern of resource usage where the allocated CPU quickly maxed out, remaining high most of the ...
8
votes
1answer
125 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 ...
11
votes
0answers
70 views
Bioisosteric replacement using SMARTS (KNIME and RDKit) [closed]
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
93 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 ...
13
votes
2answers
184 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
1answer
487 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 ...
9
votes
1answer
297 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 ...
11
votes
1answer
122 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
313 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 ...
10
votes
0answers
93 views
I have access to 1000 cores across 10 nodes, what would be the best way to prallelize an MP2, GW, or RPA calculation for a periodic system in VASP? [closed]
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
381 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
42 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 ...
10
votes
2answers
85 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
114 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 ...
10
votes
1answer
90 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 (...
21
votes
2answers
799 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
68 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
288 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
752 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 ...
8
votes
1answer
146 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:
...
10
votes
0answers
68 views
What are the methods of modeling Jahn-Teller effects in a solid-state material? [closed]
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
131 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
200 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 ...
16
votes
3answers
430 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
176 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
107 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 ...
