Questions tagged [computational-chemistry]
For questions about computational chemistry.
323
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Problematic optimization of excited states
I work with Orca 5.0.4 (without access to version 6.0) on a symmetric metal-centered system. I'm currently running excited state optimizations, and while S1-S3 and T1, T2, and T4 have optimized ...
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Franck-Condon Gaussian16 Input Advice
I am currently following page 367 of the third edition of the gaussian electronic structure software textbook. I followed the procedure laid out for performing a Franck-Condon analysis, but I am ...
MrAmateurChem
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Where is the 6D-QSAR software Quasar(X) available?
Background: I'm working on a computational chemistry / drug discovery project and am interested in testing out different methods for doing QSAR/QSPR calculations on a set of published compounds I have ...
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How to model drug adsorption on nanomaterial?
I have a substance, a Cu-bisphenanthroline complex, and I want to examine its adsorption on different materials. I am considering carbon and silica, and possibly something else like liposomes to ...
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What are some open problems to give interns?
Background: I'm a PhD student in Europe. Currently working on method/code development for computational chemistry. I have experience in DFT, code optimization, MD and Machine learning. But I'm not ...
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NAMD simulation NPT pressure fluctuation [duplicate]
I've made a simulation in NAMD in NPV.The pressure mean Is equal 1 but there Is a great fluctuation of values how can i fix It?
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Should I include H atom into C3N5 when i am doing DFT modelling?`
My experimental XPS analysis reveals that my C3N5 sample contains an N-H bond. Consequently, it is essential to incorporate the N-H bond into my DFT modeling to accurately reflect the experimental ...
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Mixing functionals in TD-DFT opt
I work with copper complexes containing at least 100 atoms (including a single Cu, nitrogens, carbons, and hydrogens). According to Grimme's paper, the benchmark level for geometry optimization is ...
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Determining bonding characteristics of a structure from PDOS
Recently, I have been working with PDOS. I can read and understand PDOS to some extent, but I am not an expert in it. These are some of the graphs I have been working on. Can someone explain how to ...
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Two imaginary frequencies in transition state obtained by CI-NEB method
What should we do when we get two imaginary frequencies in the transition state obtained using CI-NEB? For example, I looked into the CO+O -> CO2 step on 3X3 Pt(111) with sufficient vacuum slab. ...
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Workflow for modelling the final prodcut of a chemical reaction
I have done some DFT simulations before in cp2k and siesta but the kind of systems I am about to study is new to me so I would appreciate it if I got helpful suggestions from the experts.
The system ...
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Why does Car-Parrinello molecular dynamics not need an SCF procedure at every time-step?
Reading the various terms of the Lagrangian in CPMD I'm trying to understand why there is not an SCF procedure hidden there.
In fact, it seems to me like the second term of the Euler-Lagrange equation ...
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Do oscillator strengths matter when matching theoretical and experimental outcomes?
I use ORCA to do TD-DFT studies. The experimental maximum absorption is esteemed to 445.0nm . Benchmark computations were conducted and this is the exemplatory (part of) the output:
...
- 523
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DOS calculation with QE
I am doing a DOS calculation via QE and the following is my SCF file :
<I'll add it later>
My nscf file :
<I'll add it later>
My DOS file:
<I'll add it later>
My SLURM submission ...
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"Any further DFT definition will be discarded. Please, verify this is what you really want" error in elecuting &PROJWFC calculations
I encountered an error while executing the PROJWFC script. I have successfully run PROJWFC calculations on my computer for smaller systems without any issues. However, this error occurs only when ...
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(AMBER) Questioning how mask works in MMPBSA
Note: this question was also posted on the AMBER mailing list, but I reposted this question here because I needed answers for this question quickly. Sorry if this is violating any rules...
Dear AMBER ...
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Assessing excited state lifetime with TD-DFT
My question is brief — is it possible to estimate excited state lifetimes using computational chemistry (DFT/TD-DFT) tools? I am aware this may be a rough approximation (e.g., neglecting non-radiative ...
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Theoretical explanation on calculating 'total magnetic moment' and 'absolute magnetic moment' in Quantum ESPRESSO
Could someone please provide a comprehensive theoretical explanation of how Quantum ESPRESSO calculates the total magnetic moment and absolute magnetic moment of a material, as well as the ...
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327
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What is the computational scaling of DFT energy vs gradient vs Hessian?
I am trying to understand the computational expense of calculating only the energy, versus the gradient/Hessian of the DFT energy with respect to nuclear coordinates. How do these scale with the size ...
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AMBER fails to generate parameters
I'm new to computational chemistry, and I'm trying to model the enzyme EGFR and a molecule named lapatinib with AMBER. I got a .pdb file of Lapatinib attached to EGFR, and a .sdf file of lapatinib ...
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Adding a molecule in AMBER
I'm new to computational chemistry. I want to model the enzyme EGFR and a small molecule Lapatinib. I got a .pdb file of EGFR at the Alphafold website, and got a .sdf file of Lapatinib at the pdb site....
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Born oppenheimer approximation error
I got this exam question including BOA:
'rank the molecules according to increasing error value of the Born-Oppenheimer Approximation: H2, Cl2, F2, KCl, PtCl4, CH4'.
my rank is:
H2, CH4, F2, Cl2, KCl, ...
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Denticity of Molecule from Chemical or 3d structure
I'm trying to either develop or find a code which can take the picture or mol2 file of a chemical and calculate the denticity from it. How can I proceed with it or does a code do that which is already ...
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How to use rigid scan with dummy atoms in gaussian?
I am trying to use rigid scan using gaussian 09. In my case, there are three water molecules and I have placed a dummy atom at the centroid of the three water molecules. For simplicity, I want to ...
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DFT simulations of UV-VIS spectroscopy for Semiconducting Heterojunctions
I have a course project that involves DFT. Does anyone know of any tutorials or resources to simulate UV-Vis spectroscopy of semiconducting heterojunctions using ORCA, Quantum Espresso, or any other ...
RKVR14
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291
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File extension difference of 'charge-density' file created by remote servers and personal computers
Recently, I ran an SCF calculation on a remote server, expecting to run an NSCF calculation afterward. So far, all the SCF calculations I have run on my personal computer have produced a 'charge-...
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Why is the SCF calculation performed after VC-RELAX more energetically stable than the VC-RELAX calculation in QE
Recently, I performed a vc-relax calculation in QE. After vc-relax, I performed an scf calculation, including all the optimized parameters from the vc-relax output file (cell parameters, atomic ...
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Which quantum chemistry codes have the capability use point charges in a QM/MM setting?
I came across a few examples like:
NWchem : QM/MM Bq charges
PySCF : QM/MM with MM charges
GPAW : External Point charge potential
I wanted to know of other code examples, which had the same ...
- 1,105
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Investigation of ferro, ferri, antiferro, para and dia magnetism using QE
Can Quantum ESPRESSO be used to investigate ferromagnetism, ferrimagnetism, antiferromagnetism, diamagnetism, and paramagnetism? If so, could you please elaborate on how these types of magnetism are ...
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Calculating structural stability of a doped plane
The following image indicates an equation published on a reserach paper which was used to calculate structural stability in a metal atom-substituted graphene sheet. Can anyone tell me if we should ...
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Time efficient way of conducting vc relax calculations while mainting accurate results at the same time
I believe this VC-relaxation calculation will take a significant amount of time to successfully complete. Referring to the literature (which indicates that the vanadium substitution atom is positioned ...
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Formation and Optimization of Dimers, Trimers, Tetramers, and Beyond
Can anyone please mension what is the procedure to computationally create clusters such as dimers, trimers, or tetramers for Quantum ESPRESSO calculations.
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Does the size of atoms influence the speed of DFT calculations when comparing systems with almost the same number of atoms
How does the size of atoms within a structure influence the speed of DFT (Density Functional Theory) calculations?
considering that the calculation speed is known to scale cubically with the number of ...
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What major advances in theoretical and computational chemistry have been made in recent decades?
Computational modeling has become a mainstay in chemistry, materials science and physics. However, the methods that are typically employed are already decades old: for instance, the B3LYP and PBE ...
- 20k
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How to interpret defect formation energy diagram?
Why are formation energy diagrams typically plotted as a function of Fermi energy, and how should one interpret the changes in the x-axis before the charge state changes in these diagrams?
Figure ...
user10165
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At what point in the Hartree-Fock formalism is the Fock operator introduced?
I seem to be having a conceptual problem with HF theory as to where the Fock operator comes from. In order to explain the context of my conceptual problem, I will include how HF was derived according ...
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Normalization of the Smooth Overlap of Atomic Positions (SOAP) Kernel
I am using the DScribe implementation (https://singroup.github.io/dscribe/latest/tutorials/descriptors/soap.html) of the Smooth overlap of atomic positions (SOAP) ...
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Stopping an ongoing relax calculation with provision to continuing the calculation later on from that checkpoint
How can I interrupt an ongoing relaxation calculation in Quantum ESPRESSO on my system, while ensuring that I can resume it later from the same point?
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Structural stability of Graphene
is it acceptable if I came up with around -8.5ev/atom for cohesive energy of graphene?, Literature is in the range 7.3-7.9 ev/atom
The formula used for cohesive energy calculation
Codes I have used
...
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Can we use formation/ cohesive energy to express the structural stability of a supercell?
I have created a graphene supercell using Quantum Espresso and performed a vc-relaxation on it. Now, I need to verify whether the created structure is stable and demonstrate its stability with ...
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Why am I getting wrong information about basis functions on running gaussian calculation using the 6-31G basis set for the krypton atom?
This is the information about basis functions which I am getting on doing Gaussian calculation. But according to the best of my knowledge Kr has six primitive Gaussians for 1s, 2s,2p, 3s, and 3p ...
user139977
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Why my Relax calculation is not stopping?
I am conducting a relaxation calculation on a mono-layer of MoS2 with a 3x3x1 super-cell, where one Molybdenum (Mo) atom is substituted with a Palladium (Pd) atom defect. However, the calculation is ...
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Introducing a vacuum space in z direction for 2D monolayer calculations
Is the introduction of a vacuum in the z-axis necessary when utilizing a 2D monolayer material for Density Functional Theory (DFT) calculations in Quantum Espresso? (This is due to the fact that only ...
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Comparing results of various DFT calculations in Quantum ESPRESSO
To verify the reliability of calculation scheme, I want to compare lattice constants, bond length and band gap calculated by the different functionals with the experimental results.
So in order to do ...
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Error in 2D Ewald sum for a multipolar expansion
I am attempting to calculate the potential of a particle at the center of an infinite two-dimensional lattice as per the following reference:
Reference: Lambin, PH & Senet, P. Ewald Summation of ...
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vc-relax calculation on two-dimensional slab
Is performing only a relaxation calculation (calculation='relax') sufficient for geometrical optimization in conducting a density functional theory (DFT) study of ...
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Non-monotonic behaviour in calculation time with changing 'degauss' value of 'cold' smearing
"I conducted a convergence test for the degauss value in Quantum Espresso input with smearing = 'cold'.
The results, ...
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Understanding algorithm of Quantum ESPRESSO from scratch
As someone new to this field, what are some effective strategies or resources I can utilize to study and understand the Quantum ESPRESSO algorithm from scratch?
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At a particular K-point (Monkhorst Pack) grid, SCF calculation is not converging
During a convergence test of (MoS2 2x2x1) monolayer using Quantum ESPRESSO, I tried several K-point Monkhorst-Pack grids. According to my understanding, the calculation time and computational cost ...
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