Questions tagged [molecular-modeling]

Questions to do with molecular modeling.

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Orthonormality of AOs and MOs in PySCF

I have a basic question about how to calculate molecular-orbitals from atomic-orbitals in PySCF using the self-consistent field approach. My understanding mathematically is as follows: we start with a ...
Solarflare0's user avatar
7 votes
1 answer
288 views

Why use PySCF/OpenMolcas instead of VASP/QuantumESPRESSO

While I am aware that VASP and QE are widely used for solid-state materials and PySCF/OpenMolcas are primarily designed for molecular systems. I want to know why should I use PySCF/OpenMolcas for ...
Jaafar Mehrez's user avatar
4 votes
0 answers
67 views
+50

Solvation_analysis subpackage for MDAnalysis multi-atom solute

I have a simulation trajectory from DFTB+ for 1 NaNO3 in 32 H2O molecules. The trajectory is in xyz format and I converted a frame of xyz to pdb using openbabel to serve as topology input. I am ...
bhopshang's user avatar
  • 233
3 votes
1 answer
53 views

Creating a Hypothetical Hexagonal Monolayer Structure Similar to MoS2

I am seeking guidance on how to generate a POSCAR file for a hypothetical monolayer with a hexagonal structure similar to MoS2. Can anyone provide me with a step-by-step procedure or recommend any ...
Farah Shehzadi's user avatar
5 votes
1 answer
138 views

MOPAC: Is there a simple way to display geometry trajectories

I would like to display MOPAC geometry trajectories for structure minimization and transition state searching. Is there a simple way to achieve that ? Avogadro can display only final geometry from ...
Miro Iliaš's user avatar
4 votes
1 answer
363 views

Blind docking and targeted docking

I used Autodock Vina and UCSF Chimera to perform blind and targeted docking on a protein from the RCSB database and a molecule I had optimized with Gaussian software.The results are as follows: The ...
sarra6's user avatar
  • 579
4 votes
0 answers
54 views

CCSD calculation between two orbitals

I am trying to calculate the CCSD energies between two orbitals. Suppose I have a system, ...
Pro's user avatar
  • 934
3 votes
1 answer
74 views

Making Deuterium POTCAR file for optimization in VASP software

How to make Deuterium POTCAR file? i have Hydrogen POTCAR file.
Rubi Agrawal's user avatar
3 votes
1 answer
79 views

Cannot reproduce excitation energies in Orca

I do TD-DFT studies in Orca 5.0.3 on porphyrin system and hence at the very beginning I need to pick functional that reproduce excitation energies. The experimental reported values equal: 691, 656, ...
farmaceut's user avatar
1 vote
1 answer
71 views

What is the best way to optimize molecules with 8000 atoms. This includes C,H,O,N,Si

My molecule includes C,H,O,N,Si
AKM's user avatar
  • 11
2 votes
1 answer
19 views

Geometry of H2O in the v=1 vibrational state for AIMD simulation

This is a follow-up to my recent question: Algorithm for finding the v=1 state of an H2O molecule I want the geometry (atomic positions) of the H2O molecule in the v=1 state. How are initial ...
Nidhi Tiwari's user avatar
1 vote
0 answers
22 views

Error with running GROMACS with SLURM

I am running into errors while submitting a job for a basic MD Simulation with HPC on SLURM. My sbatch script reads as follows: ...
Pranoy Ray's user avatar
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1 vote
1 answer
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Algorithm for finding the v=1 state of an H2O molecule

In the context of simulating the dissociation dynamics of an H₂O molecule on a metal surface, what algorithm is employed for generating the initial state of a tri-atomic non-linear molecule, such as H₂...
Nidhi Tiwari's user avatar
4 votes
0 answers
62 views

What do Negative Atomic Orbital Contributions in a Mulliken Population Analysis mean?

I am performing a Mulliken population analysis (MPA) for a molecular system of interest (calculated with B3LYP/Def2-TZVP). I am analyzing the LCAO-MO coefficients/contributions associated with each &...
Kevin Freddo's user avatar
4 votes
1 answer
81 views

How to orthonormalize a set of Molecular orbitals?

I am using PySCF, and checked that the molecular orbitals(MO) from the HF calculation are orthonormal. If S is the Overlap matrix, and V is the matrix of the MO coefficients, It can be seen from the ...
Pro's user avatar
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6 votes
2 answers
393 views

How may I solve the radial Schrödinger equation?

I want to solve the radial Schrodinger equation for a Carbon atom with all six electrons. The equation I want to solve is for $r>0$: $$[\frac{-\hbar^2}{2m}\frac{\partial^2}{\partial r^2}+ \frac{\...
L Maxime's user avatar
2 votes
1 answer
125 views

Choice of SMASS for AIMD simulations in VASP

How can one verify that the values (0, 1, 2, and 3) in the SMASS parameter correspond appropriately to the NVT ensemble(Nose-Hoover thermostat) in the context of an ab initio molecular dynamics ...
Rubi Agrawal's user avatar
7 votes
2 answers
159 views

Why is electron correlation called the "chemical glue"?

A significant part of quantum chemistry involves developing methods that go beyond the Hartree-Fock theory which treats electron-electron interactions through a mean-field approach. From what I ...
Fracton's user avatar
  • 271
3 votes
1 answer
137 views

having trouble to get the NPT working

I am currently encountering challenges in successfully conducting NPT simulations in LAMMPS for a triclinic cell persistently remain unchanged throughout the NPT simulation.my input file is: ...
Ati's user avatar
  • 31
4 votes
1 answer
60 views

Povray rendering of Jmol visualization appears brighter

I would like to use Povray to render nice-looking graphics of molecules, which can be exported from visualization softwares like Jmol. However, I have noticed that the color of the rendered graphics ...
Jingyang Wang's user avatar
7 votes
1 answer
71 views

Numerical atomic orbitals vs Gaussian-type orbitals for molecular calculations

Gaussian-type-orbitals (GTOs) are the work horse of modern molecular quantum chemistry calculations. They are computationally efficient and allow for analytic evaluation of integrals. However, there's ...
Fracton's user avatar
  • 271
2 votes
1 answer
44 views

How to make initial trajectory for incident A2 molecule on any surface?

I want to write code to simulate the impingement of any molecule on a surface at different (r, theta, and phi) angles in XYZ format.
Rubi Agrawal's user avatar
5 votes
1 answer
161 views

How to convert MoO3 bulk structure to MoO3 (010) plane surface via VESTA software?

Convert MoO3 bulk structure to MoO3 (010) plane surface via VESTA
Rubi Agrawal's user avatar
6 votes
1 answer
92 views

Is it essential to include solvent cage effect in radical reactions?

My question is straightforward and is outlined in the post title: Is it essential to include the solvent cage effect in radical reactions during the computational estimation of Gibbs free energies and ...
farmaceut's user avatar
5 votes
1 answer
47 views

Generating a pseudopotential for graphene: Is it done on an individual carbon atom, or on an entire unit cell of graphene?

Let's take the example of a 2D graphene layer. The objective is to do an electronic calculation with only the valence electrons with a plane wave basis. Hence the need to pseudize the core electrons ...
mle's user avatar
  • 989
4 votes
2 answers
130 views

Post-hartree fock calculation with localized Molecular orbitals in PySCF

I have localized the canonical Hartree-Fock orbitals for a molecule in PySCF. Now I want to perform ccsd calculations with these localized orbitals. Is it possible with pyscf? Example with CCSD with ...
Pro's user avatar
  • 934
6 votes
0 answers
62 views

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 ...
sunfishstanford's user avatar
3 votes
0 answers
67 views

Using GPyTorch for GPR together with the SOAP-Kernel

My goal is to use a Gaussian Process Regression (GPR) model with the GPyTorch library with the SOAP (smooth overlap of atomic positions) descriptor that can be obtained with the DScribe library. I ...
C_Swann22's user avatar
  • 573
3 votes
0 answers
44 views

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 ...
Imane Yamari's user avatar
3 votes
0 answers
110 views

Advise in generating ESP surfaces from Gaussian .cube files using the IQmol software

I am trying to generate an ESP surface of a Gaussian09 calculation using the iqmol software. I have used Gaussview to visualize the ESP surface by generating .cube files from .fchk files (using the ...
Kevin Freddo's user avatar
6 votes
1 answer
144 views

How are 2-electron integrals usually computed?

I want to compute 2-electron coulomb integrals. When the Primitive Gaussian is not centered at 0, my quadrature scheme fails unless I increase the number of quadrature points. I am currently using a ...
mle's user avatar
  • 989
10 votes
1 answer
361 views

Inconsistencies in a famous point group table

The original resource "Tables for Group Theory" By Peter Atkins, Mark Child and Courtenay Phillips (1970). I have been using this 2008 version, in which Pg. 37 has the following table: Some ...
Nike Dattani's user avatar
  • 34.7k
2 votes
1 answer
48 views

Does the relaxed density (and therefore the relaxed orbitals) depend on the final energy in OO-DHDF+D calculations?

During an OO-RI-ωB97X-2-D2 calculation on ORCA, the non-dispersion-corrected OO-DHDF part of the calculation is performed, the D2 dispersion correction energy added to the resulting OO-DHDF energy, ...
Kanghun Kim's user avatar
2 votes
2 answers
51 views

Specify Molecular Visualization Dimension

I'm using Chemistry Development Kit (CDK) to create molecular drawings using the DepictionGenerator class. It allows me to set the drawing's width and height using the method withSize(w, h) but the ...
Velusamy Velu's user avatar
5 votes
1 answer
774 views

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 ...
Cro's user avatar
  • 51
3 votes
1 answer
103 views

How is the LUMO lower energy than the HOMO for triplet state restricted-open shell DFT calculation?

I recently ran a calculation using the ROB3LYP/LANL2DZ level of theory for a triplet spin molecule. While analyzing the results, the HOMO is doubly degenerate and the LUMO is singly degenerate. I ...
Kevin Freddo's user avatar
6 votes
2 answers
115 views

Is there any Python library for returning the atoms of a periodic material within a cube?

Is there any Python package that allows to cut defined by the points (0, 0, 0) and (x, y, z)? That is, it should return all the atoms of the unit cell and periodic images inside the shaded region. (...
ado sar's user avatar
  • 211
3 votes
1 answer
149 views

Saving forces from ASE Molecular Dynamics calculations

I have run some molecular dynamics calculations with a pretrained machine-learning potential (M3GNet) which uses the ASE MolecularDynamics calculator. My goal is to compare the results (energies and ...
Jingyang Wang's user avatar
5 votes
1 answer
129 views

Calculating theoretical density from .cif files

I'm studying structure-property relations in MOFs and have a pool of hypothetical structures in .cif format generated using ToBaCCo code. I want to filter them based on theoretical density, but the &...
hari's user avatar
  • 83
4 votes
2 answers
103 views

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 ...
farmaceut's user avatar
  • 536
3 votes
1 answer
74 views

How to exploit STO-nG coefficients from basissetexchange (BSE)?

I am trying to understand how to use the data of STO-6G basis from BSE in order to code my own DFT package. I started with a simple DFT code for H2. So the primitive gaussians are of the from : $$\...
mle's user avatar
  • 989
3 votes
1 answer
143 views

Order Parameter for Water in an MD Trajectory: Understanding Changes in Oxygen-Oxygen-Oxygen Triplet Angular Distributions

I'm interested in understanding how changes in the oxygen-oxygen-oxygen (O-O-O) triplet angular distribution can provide insights into the order parameter. In literature, the tetrahedral order ...
Saha_1994's user avatar
  • 969
6 votes
1 answer
128 views

Use of genetic algorithm based methods for geometry optimization

What are the benefits or pitfalls in using a GA based optimizer for geometry optimization instead of a more traditional Hessian based algorithm? It can be argued that performing single point energy ...
Hemanth Haridas's user avatar
2 votes
1 answer
62 views

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 ...
farmaceut's user avatar
  • 536
2 votes
1 answer
234 views

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.
Shelby Franke's user avatar
3 votes
1 answer
44 views

Creating a beta cristobalite with 200 or fewer atoms

Can someone suggest me a method to generate a beta cristobalite structure with atoms less than 200.? I tried VMD's inorganic builder tool but so far unsuccessful.
Xdrake's user avatar
  • 531
3 votes
1 answer
86 views

Electric-field/ length gauge : momentum displacement property

I am learning about the Theory of intense laser-induced molecular dissociation. To set the notations, the radiation field Hamiltonian is for a single charged particule : $$H = \frac{1}{2m}(p-q\hat{A}(...
mle's user avatar
  • 989
3 votes
0 answers
43 views

How to draw multiple Lewis structures from the same molecular formula?

I am learning about Lewis octet theory and the following formulae were shown as guidelines to draw Lewis structures: $$ \begin{align} V &= \text{total valence electrons}\\ R &= \text{required ...
ananta's user avatar
  • 191
4 votes
1 answer
125 views

LAMMPS error "Two fix ave commands using same compute chunk/atom command in incompatible ways"

I am very new to using LAMMPS. I am trying to obtain some simulations. I was using an older code which had ave/spatial fix style. In the new LAMMPS version it doesn't work so I am switching to ave/...
Gaurav Maurya's user avatar
3 votes
1 answer
104 views

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'...
farmaceut's user avatar
  • 536

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