Questions tagged [computational-chemistry]
For questions about computational chemistry.
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How do you run Gaussian's cubegen with multiple processes/threads?
The cubegen manual gives the signature of cubegen as:
cubegen nprocs kind fchkfile cubefile npts format cubefile2
Where:
nprocs
Number of shared memory ...
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1
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Absorption enthaply at different temprature in VASP software via ab initio molecular dynamics
Can we calculate the absorption enthalpy at different temperature in VASP software via ab initio molecular dynamics? If yes, how?
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How do you determine the Pull Direction for a GROMACS umbrella sampling simulation to generate the most accurate free energy value?
I am trying to calculate the free energy between a protein and aptamer using GROMACS. Literature has indicated that one of the best way to do so is by performing an umbrella sampling MD simulation ...
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When optimizing AMBER molecular dynamics parameters for protein-ligand interactions, how do I balance accuracy and efficiency?
Are there established practices for fine-tuning AMBER MD parameters in scenarios like mine, involving specific factors like mutant proteins or non-standard ligands? Has anyone successfully tackled ...
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Updated book/chapter or review article with broad perspective on computational chemistry
I really like Frank Jensen's "Introduction to Computational Chemistry" because it provides a broad perspective, starting from first principles and extending to surveys of current methods for ...
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Difference between pi-pi* transition and intramolecular charge transfer ICT in organic solar cells?
Intramolecular charge transfer (ICT( occurs from donors to acceptors in molecules. This phenomenon can be observed by visualizing the charge distribution patterns of HOMO and LUMO. While studying D-A ...
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How do you calculate a full quartic force field for anharmonic frequencies?
I am an experimental chemist interested in anharmonicity—I am particularly interested in how to calculate anharmonic frequencies. The method I have the most experience with is (generalised) second ...
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Running molecular docking simulation between two proteins
i did run docking simulation between two proteins on HADDOCK server
but now i want to run a simulation of complex (protein+ligand and protein) is it possible with HADDOCK and how can i use it
best ...
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Database on calculated molecular vibrations including coordination complexes?
Related to the question Are there dashboards displaying experimental properties of molecular materials?
My question is: Are there any good, free, online databases on calculated vibrational modes of ...
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OOM Error Calculating ESP Charges with Psi4
I'm trying to create a script to generate partial charges for a given .dat file.
As an example of my process, I'm currently using gromacs to run minimization on a box of propane. It outputs a min.gro ...
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Identifying Key Chemical Series, Pharmacophores, and Scaffolds in a Large SDF Dataset
Hello fellow computational chemists!
I have encountered a challenge that I'd like to discuss and seek advice on. Suppose I have a substantial dataset in SDF format containing thousands of molecules. ...
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How much should you shift fragment energies to create an energy level diagram?
I am creating an energy level diagram for the orbitals of [XeF₅] - molecule produced by two fragments: [Xe] 4+ and [F₅] 5-. There is a very large energy difference between the two fragments, so I ...
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How can I properly plot this .cube file in Python?
Motivation for Post: I saw a question about how to plot a .cube file recently on the Mathematica & Wolfram Language Stack Exchange. It was marked "off-...
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Energy of formation Vs Formation Energy Vs Heat of Formation Vs Energy Above Hull differences
I work in the field of materials science. While exploring the concepts related to material stability, I have come across terms such as "Energy of Formation," "Formation Energy," &...
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Why the total energy calculated with GGA and metaGGA=SCAN are so different?
Why the total energy calculated with GGA and metaGGA=SCAN are so different?
My INNCAR file is
...
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Error Simulating bulk diemthyl-ether with angle constrain in gromacs
I am trying to simulate bulk dimethyl ether with total constraints, both bonds and angles.
I am using lincs with constraint = all-angles in *.mdp file in gromacs.
I am attaching the error I ...
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Why are Coulomb interactions modeled with just r, not r squared?
As far as I understand (as a complete beginner to molecular simulation and modelling), Coulomb's law for two atoms i and j is:
$$F=k\frac{q_iq_j}{(r_{ij})^2}$$
(the force is proportional to the ...
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Analytical derivative of nuclear-electron attraction integrals over gaussian functions
I'm currently writing a program which evaluates the first derivatives of molecular integrals (over gaussian basis sets) with respect to the cartesian coordinates of the nucleus. I'm somewhat stuck ...
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How to fit Smooth Overlap of Atomic Positions (SOAP) into Kernel Ridge Regression (KRR)?
I have a dataset of 64 chemical structures and their calculated energies, which I want to predict using machine learning. I need to use SOAP as a descriptor so that each structure would be an ...
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Basis set of the overlap, kinetic, electronic matrices for RKS, UKS and ROKS code: O2 and NO2 cases
This question is a follow-up of this post.
The basis set to approximate the overlap, kinetic, electron repulsion and proton-electron attraction matrices is to be choosed by the user depending on the ...
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What is the Atomic Orbital (AO) basis of the (overlap, kinetic, electric) matrices of the RKS, UKS and ROHF?
I am trying to code a simple UKS program. For RKS code, the AO basis functions are set of the spatial part of the wavefunction of every atom involved in the molecule. For ${H_2}$, this is the two ...
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Help setting the input geometry into standard orientation for a single point g09 calculation
I am trying to run a single point g09 calculation for a pentagonal planar molecule with D5h symmetry using the B3LYP/LANL2DZ level or theory.
I would like the calculation to use symmetry, however the ...
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Advice on converging a restricted open-shell DFT (rob3lyp/LANL2DZ) single point Gaussian09 calculation for a triplet spin-state molecule?
I am running a single point calculation on a fragment of a molecule using restricted open-shell theory. The fragment is in the triplet spin-state and of pentagonal planar structure (D5h). I ran the ...
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How to choose the orientation of basis functions in a Gaussian calculation?
I am trying to run a g09 calculation for a D5h symmetric molecule using the HF/LANL2DZ level of theory. The molecule is pentagonal planar in geometry, and I would like to visualize the canonical ...
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Complex formation site between polymer and external compound
I am studying about conjugated polymers in sensors applications. I want to conduct structural of complex and its properties (such as HOMO-LUMO etc.). Is there any software for docking that external ...
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Why is chemical bond dissociation difficult to simulate?
I'm a student doing quantum computing research trying to understand better what kinds of chemical systems are difficult to simulate on a classical computer and for which quantum simulation could be ...
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Resource recommendation for learning matter modeling for a novice [closed]
I am a starting researcher in condensed matter physics. Hence, i have all the necessary background regarding quantum physics, and condensed matter physics. But what i want to do is to learn different ...
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2
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Cannot optimize hexa aqua Cu(II) and Fe(III)
I try to optimize very simple systems - hexa aqua Cu(II) and hexa aqua Fe(III) - in Gaussian 16. The inputs are provided in the end of the post. Unfortunately, the geometry optimization never finishes ...
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VASP - suggestion on optimization of interfaced slabs
I am currently trying to create a CeO2 (100) / CoO (200) interface for a bulk oxide.
Unlike what I usually see, slabs stacked on the z-axis ("vertically"), I would like to stack the two &...
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Establishing AAs protonation - which software to choose?
I need to establish protonation of aminoacids composing the studied protein. To my knowledge there are H++ and Pdb2pqr servers that are able to do that. However, they yield quite much different ...
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How to calculate ionic radius in Gaussian?
I am working with lithium sulfate and am wondering how to figure out the ionic radius of the Li atoms. I did a DFT/B3LYP/G-311G ++ (d,p) calculation.
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How accurate is DFTB+ in reproducing DFT result?
I am trying to study the shifts in the Fermi level of a graphene - ssDNA hydrid system, depending on the identity of the ssDNA. The structures are obtained from a classical MD simulation, and cannot ...
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How do you make sure the reaction is diffusion limited (Gaussian)?
I am investigating the mechanism of hydrogen transfer between a hydroperoxyl radical and an aromatic hydroxyl group donating it. The problem is that I cannot find transition state structure. So far, I'...
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What kinds of calculations have to execute for obtaining the velocity of the chemical precipitation of some salt on a thread from a water-salt mix?
Some salt ($\ce{NaCl}$ or another one) of $m$ grams is dissolved in some water of $V$ liters. After mixing up, the substance looks transparent or to put it more exact as a chemical solution. Then a ...
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Determination of fluorescence lifetime by using oscillator strength?
$$k_r=2.88\times10^{-9}n^2\langle\tilde{v}\rangle_\text{av}^2 \int\varepsilon_{\tilde{v}}d\tilde{v}$$
$$f=4.32\times10^{-9}\int\varepsilon_{\tilde{v}}d\tilde{v}$$
I plan to use the above equations to ...
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What is the minimum number of atoms required to run a Monte Carlo simulation meaningfully?
What is the minimum number of atoms required to run a Monte Carlo simulation meaningfully?
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Error in UCCSD(T) Calculation in PySCF for S atom?
I am trying to calculate the UCCSD energy and UCCSD(T) correction for the S atom using PySCF. Using sto-3g basis set, I found that the UCCSD calculation would be completed successfully, but the ...
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Loading Gromacs Trajectories using ASE (Atomic-Silumation-Environment)
I am trying to study some trajectories generated using Gromacs. I have been given tpr and pdb files of the simulation. What might be the most effective way to load them in ASE? Or is there way to ...
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How to remove f functions from a cc-pVQZ basis set in CFOUR format?
I need to perform a calculation on a BN system with using cc-pVQZ stripped of the f functions. However, I don't really know how to do this and I have not been able to find a revised one already. I ...
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Quantum ESPRESSO vs AMS [closed]
Both Quantum ESPRESSO and AMS (Amsterdam Modeling Suite) can be used to perform simulations of the materials and their properties. What are the differences between AMS and Quantum ESPRESSO? Is it ...
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What are the general principles of setting parellelization options in VASP?
I am doing the computation of a perovskite system of 20 atoms in a supercell.
I know that options like NPAR and KPAR, and the numbers of cores used for computations can greatly affect the efficiency, ...
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What should be the criteria of convergence over ENCUT?
For example, should a computation be considered to converge when the differences in energy per atom are smaller than a certain value?
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Is it a good idea to always read charge and orbitals if I am working on similar systems?
For example, if I am investigating of the elastic properties of a crystal by doing a lot of computations of crystals applied with small strain.
Also, is it a good idea to read charge and orbitals when ...
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Does PySCF use chemist's or physicist's notation for 1- and 2-electron integrals?
I am trying to evaluate 1- and 2-electron integrals using PySCF trough this code:
Hij = mol.intor('int1e_kin') + mol.intor('int1e_nuc')
Vijkl = mol.intor('int2e')
...
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Why are my HPC calculations not running in SLURM?
Question
I submitted 2 jobs for the first time in a HPC to test it. It's a very light calculation that takes almost 5 minutes or less in my desktop. But it has been almost 1 hour since I submitted the ...
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Smooth overlap of atomic positions (SOAP) output for Gaussian Process regression in sklearn
I want to use the smooth overlap of atomic positions (SOAP) as a descriptor to represent the atomic environment of a specific atom to predict chemical shifts. I have generated averaged SOAPs for ...
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MPI error in Quantum ESPRESSO during optimization of particularly large molecules
I have been recently trying to optimize a particularly large system Mo2C in QE using the pw.x executable and encountering the following MPI errors:
...
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How to calculate charge transfer (CT) in NBO Analysis using Gaussian 09?
I have a coronene structure, functionalized with hydroxyl groups.
I want to calculate the charge transfer (CT) between the coronene and the hydroxyl group, using NBO analysis as implemented in ...
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Question on CPU timings and/or ratio resp. DLPNO-CCSD(T) and wB97X-2-D for protein of ca. 1M Da
Suppose one has a protein of about 1 million Da, and performs a DLPNO-CCSD(T)/def2-TZVPPD/AutoAux/AutoAux calculation, and then performs a wB97X-2-D/def2-TZVPPD/AutoAux/AutoAux calculation, both via ...
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DFTB+ parameters for additional atoms
I wonder if anyone here knows about additional atomic parameters and interactions sets for atoms not currently present in the DFTB parameter sets. The parameter sets are located at DFTB parameters. ...
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