Questions tagged [molecular-modeling]
Questions to do with molecular modeling.
179
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9
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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 ...
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2
votes
1
answer
32
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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, ...
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2
votes
2
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48
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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 ...
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5
votes
1
answer
745
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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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3
votes
1
answer
48
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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 ...
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2
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99
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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.
(...
- 211
3
votes
1
answer
74
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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 ...
5
votes
1
answer
59
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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 &...
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4
votes
2
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101
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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 ...
- 536
3
votes
1
answer
69
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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 : $$\...
- 495
3
votes
1
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58
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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 ...
- 919
6
votes
1
answer
105
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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 ...
- 2,612
2
votes
1
answer
46
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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 ...
- 536
2
votes
1
answer
96
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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.
3
votes
1
answer
41
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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.
- 481
3
votes
1
answer
81
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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}(...
- 495
2
votes
0
answers
28
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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:
$$
\begin{align}
V &= \text{total valence electrons}\\
R &= \text{required ...
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4
votes
1
answer
71
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LAMMPS error "Two fix ave commands using same compute chunk/atom command in incompatible ways"
I am very new to using LAMMPS. I am trying to obtain some simulations. I was using an older code which had ave/spatial fix style. In the new LAMMPS version it doesn't work so I am switching to ave/...
3
votes
1
answer
86
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How do you make sure the reaction is diffusion limited (Gaussian)?
I am investigating the mechanism of hydrogen transfer between a hydroperoxyl radical and an aromatic hydroxyl group donating it. The problem is that I cannot find transition state structure. So far, I'...
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2
votes
0
answers
55
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Determination of fluorescence lifetime by using oscillator strength?
$$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 ...
- 21
2
votes
2
answers
111
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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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4
votes
0
answers
61
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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 ...
- 919
3
votes
1
answer
75
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Computing the kinetic energy of a molecular orbital
I want to compute the kinetic energy of the molecular orbitals computed by Gaussian 09, the variable U in this paper. Can it be computed from the orbital energy using a formula or does it need to be ...
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4
votes
1
answer
61
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Electronic structure of s-indacene
Structure shown in (a) is the regular $s$-indacene molecule, and (b) is a structure that i generated such that the central six-member ring remains similar to benzene. It is well-known in literature ...
- 2,612
4
votes
1
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280
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Atomic Simulation Environment (ASE) Modelling. Adding additional layer
Beginners here, to ASE. I've create a 2x2x2 supercell of TiO2 from unit cell (.cif file obtained from LegacyMaterialsProject ) using ASE. The script code is attached as follows. The outcome is shown ...
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4
votes
1
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69
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How to study the stability of structure in water and analyze the radial distribution function (RDF)?
Context:
If I have a system that consists of 20 structures. During molecular dynamics, these structures can form micelles from my point of view.
I would like to do the following:
Confirm if the ...
- 1,285
8
votes
1
answer
258
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Difference between Statistical Physics, Statistical Mechanics, and Molecular Modeling?
I am looking for relevant books to study the modeling and Monte Carlo simulation of protein chains.
I see that books related to Statistical Physics, Statistical Mechanics, and Molecular Modeling have ...
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5
votes
1
answer
420
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Unwrapping particle coordinates in MD simulations to remove effects of periodic boundary condition
While calculating various quantities that involves particle positions ( for example, radial distribution function, mean square displacement etc.) using Molecular Dynamics simulation, the effects of ...
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3
votes
1
answer
69
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Estimate the time between different residues?
Imagine now, I have 5 structures, and I want to estimate the time when the 5 structures are closer to each other at the same time. I thought I could extract the distance between the different ...
- 1,285
3
votes
0
answers
64
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NPT Molecular dynamics calculation problem
I am trying to heat up my system from 10K to 300K using the NPT ensemble. But the temperature doesn't reach 300K. What do you think is the problem?
This is my code for the heating part. However, the ...
8
votes
3
answers
637
views
Duplicate structure in PDB format?
I have a PDB file. I want to duplicate this pdb file automatically instead of doing it manually. For example, if I visualize my PDB, I will find only one structure in (x,y,z). I want to have more ...
- 1,285
3
votes
1
answer
312
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Merging multiple PDB files in VMD using Tcl scripts?
I am trying to generate a matrix of small molecules arranged at locations (x, y, z) on a cube. I already have a Tcl script that can generate the required PDB and PSF files. However, I was wondering if ...
- 2,612
4
votes
1
answer
103
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What does it mean by a "restraint" in the case of a protein chain?
Discrete restraint-based protein modeling and the Cα-trace problem
We present a novel de novo method to generate protein models from sparse, discretized restraints on the conformation of the main ...
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5
votes
0
answers
39
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Get kinetic diameter of a molecule
I want to calculate the kinetic diameter of a molecule to estimate if it can fit inside a pore/channel of a microporous material. Do you know any software that would allow me to do this?
I've seen a ...
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4
votes
1
answer
281
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Quantum ESPRESSO installation
People, can someone please help me how to solve this problem with QE 7.0 installation:
- 505
5
votes
3
answers
326
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Energy of each fragment in ORCA?
After the definition of the fragments in the geometry section of the calculation, is there a method to call, or a keyword to turn on, in order to obtain the energy of the fragments themselves?
...
3
votes
1
answer
94
views
How to Model Antiferromagnetic NiO p-type semiconductor?
I'm a beginner in DFT and I want to study the properties of NiO and doped-NiO materials using Quantum ESPRESSO.I found in the internet that I should introduce the spin magnetization in the Input file (...
- 1,875
8
votes
2
answers
373
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Silica (α-cristobalite) water system generation
I'm trying to model the silica-water interface using classical molecular dynamics. Hope to use LAMMPS for the simulations and CHARMM potential to model the atomic interactions. I wonder how to ...
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4
votes
1
answer
237
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Should this phenolic hydroxyl be rotatable?
Looking at nelfinavir, I get variable results from different compchem packages on whether the phenol hydroxyl oxygen should be rotatable (SP3) or non-rotatable (SP2). Which one is it?
Feasibly, there ...
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3
votes
1
answer
91
views
Model coordination complex using GROMACS or CP2K
Is it possible to compute a 3D model of a calcium EDTA complex and it's energy? If so, how should I go about doing it or where can I obtain relevant information regarding computation methods?
I ...
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2
votes
0
answers
37
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simulate liquid solvent mobility through gel polymer electrolyte
I would like to simulate a liquid solvent (such as TEGDME) embedded into a polymeric cage (such as PEGDM). What is the most meaningful approach to estimate transport properties in such system?
Is MD a ...
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3
votes
0
answers
150
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How can we build a polymer from a monomer in Avogadro?
I have been trying to reproduce a geometry optimization from a research paper, where it was done by Avogadro.
However, I cannot find the option for building a polymer from a monomer. I am using ...
6
votes
0
answers
46
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Is it possible to evaluate rotational and vibrational partition functions for diffusion in the Eyring Theory of Absolute Rates?
Let us consider the usual expression for Diffusion processes and diffusion coefficients in the Eyring's theory:
$$D=\lambda^2k = \lambda^2 \frac{k_BT}{h}\frac{\Omega_\ddagger}{\Omega}e^{-\frac{\...
3
votes
0
answers
121
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Locating Symmetry Equivalent Atoms from Distance Matrix?
As a follow up to my previous question here, I am now trying to implement symmetry detection in my code. I am following the paper by Beruski et. al to understand the background required. I am able to ...
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43
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Can an atomic structure created after a simulation performed at 251K in LAMMPS be initialized directly to 268K in a separate simulation? [closed]
I have a combined mW water and FCC111 Aluminium substrate model to study ice nucleation and adhesion. This simulation is performed at 251K which is the temperature for the actual real-world experiment....
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2
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0
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56
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how to incorporate size polydispersity in colloidal suspensions [closed]
Basically, I'm working on spherical colloids and investigating the phase behavior of these monodisperse colloids using Monte Carlo simulations (Fortran 77 coding). Now I want to introduce size ...
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3
votes
1
answer
130
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Ovito dislocation analysis
How can I append my pipeline in Ovito?
I tried to append DislocationAnalysisModifier with Selected atom:
...
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7
votes
1
answer
317
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How is the zero energy defined for molecular orbitals?
In DFT and Hartree-Fock bonding orbitals have negative energies while antibonding orbitals have positive energies. Why is this the case? It seems this is due to the zero-point energy being defined for ...
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5
votes
1
answer
50
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Generalization of always accepting box upscaling moves in Monte Carlo for a triclinic box
When you are using Monte Carlo scheme to simulate equilibrium phases of convex hard-core molecules, namely, whose energy is infinite when in contact and 0 otherwise in a standard, cubic simulation box,...
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6
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1
answer
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Rdkit: How can I get a weighted adjacency matrix where the weights are bond lengths, from the SMILES of my molecule?
Given the SMILES of my molecule, how can I get a weighted adjacency matrix where the weights are the bond lengths, using the Rdkit package and Python?
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