Questions tagged [computational-chemistry]
The branch of chemistry dealing with the use of mathematical models to solve problems in chemistry.
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Need help with the python code: Calculating Madelung constant CsCl crystal structure
Need help with the code to estimate the Madelung constant for CsCl lattice:
Cs at (0,0,0)
Cl at (0.5, 0.5, 0.5)
Answer: Converged value I am getting is 0.465. ...
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Newton-Raphson with Zeroth-Order Continuation is not Converging
I am trying to solve this system of nonlinear equations using Newton-Raphson method with continuation (zeroth-order continuation).
$F_1(x, y, \xi, \nu) = \left(1 - \frac{1}{\nu}\right) \left(1 - x\...
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Starting configuration for Molecular Dynamics
I have to build a bilayer using a structure obtained in a previous MD simulation. In the structure, some chains of the molecules cross the simulation box as shown below. I added water layers to the ...
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Choice between DAE or ODE formulation for chemical systems
Consider a simple ODE system describing the evolution of two chemical species undergoing the reaction $A = B$ :
$$ \frac{dn_A}{dt} = - k * n_A $$
$$ \frac{dn_B}{dt} = k * n_A $$
We can discretize ...
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How to perform FFT from plane-wave basis function coefficients to real space?
I have a 3D grid in real space of grid spacing $L$ and say 21 grid points in each direction, containing e.g. a charge distribution. This is stored as a numpy array of shape ...
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Good examples of "two is easy, three is hard" in computational sciences
I recently encountered a formulation of the meta-phenomenon: "two is easy, three is hard" (phrased this way by Federico Poloni), which can be described, as follows:
When a certain problem is ...
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Algorithm for constructing a supercell using an arbitrary integer matrix [closed]
Software like Diamond and VESTA allow users to build a supercell by extending the structure along the basis vectors of the latttice. However, I'd like to do something more general and build a ...
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Optimising transition state geometries using gaussian 16
I'm attempting to carry out transition state optimisations in Gaussian and a lot of my calculations are coming up with errors, the main one being
no analytic 2nd derivatives for this method.
How can ...
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Does it make any sense to acquire some sort of knowledge about manufacturing or engineering for computational design optimization? [closed]
Does it make any sense to acquire some sort of knowledge about manufacturing or engineering for computational design optimization?
I've viewed computational science to be an abstract science ...
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Calculating the species mass consumption from implicit reaction-term in diffusion-reaction equation
The 1D diffusion equation with a chemical source term has the following form:
$$\frac{\partial Y}{\partial t} = D \frac{\partial^2 Y}{\partial x^2} - k Y,$$
where $Y$ is the molar concentration of the ...
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Who can explain the minimum image convention in molecular dynamic simulations?
How to choose the cutoff radius so that the atoms do not interact with its periodic image? Especially when simulating macromolecules (proteins).
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Quasi-Newton Method with a Transformed Hessian
I've recently came across an implementation of the BFGS algorithm but it has an additional step where the Hessian is transformed after the each update. This transformation is done so that certain ...
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Examples of kinetic modeling with optimization techniques in Python
We are looking for studies or tools that implemented kinetic modeling with parameter estimation differential evolution or similar optimization techniques in Python.
We are trying to understand what ...
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What is the difference between Coupled Cluster SD and SD(T)?
Can you explain the difference between these two computational methods ?
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How does one determine the point group of a molecule?
You've managed to finally find out how the atoms are spatially arranged on your newly-discovered molecular entity. Through, say, spectroscopic means, you are now in possession of a bunch of atom ...
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How important is learning hardware/architecture for scientific computing?
Apologies if this is a bit of a soft, unclear, or opinion-based question. I'm a relatively new PhD student in a (computational) quantum chemistry group. My group develops and maintains a few software ...
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Matlab solution for implicit finite difference heat equation with kinetic reactions
I am trying to model heat conduction within a wood cylinder using implicit finite difference methods. The general heat equation that I'm using for cylindrical and spherical shapes is:
Where p is the ...
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Reference request: Textbook similar in structure to "Computational Materials Science: An Introduction" by June Lee for Computational Biology
In the Computational Materials Science: An Introduction by June Lee, he discusses molecular dynamics and density functional theory with examples from LAMMPS and QuantumEspresso, and explains LAMMPS ...
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Moller Plesset Theory- MP2 correction
I have a molecule LiBH2 with C2V point group. I used 3-21G basis set and obtained RHF coefficients and symmetry of orbitals. I wish to find the set of orbitals (a,b,i,j)( where a and b are occupied ...
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Applications of Julia in Chemistry and Molecular Physics?
I was wondering if there are any Theoretical & Computational Chemistry (MM, QM) codes or publications out there that are based primarily on the Julia programming language?
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Where can I find a database of simple chemical structures in XYZ format?
As from Title. Where can I find a database of simple chemical structures in XYZ format, possibly with a simple CAS -> XYZ or InChi -> XYZ REST service ?
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Why is scoring a separate problem even after docking is done?
With regards to protein-ligand interactions, we talk about two concepts, docking and scoring. I understand that docking means to find the best orientation of a ligand at the active site of a protein, ...
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What does it mean for a basis set to be "correlation consistent" ?
Some basis sets are said to be "correlation consistent". What does it mean in practice ?
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List of Tersoff potentials?
I would like to know some GNU libraries or lists of downloadable Tersoff potentials. I couldn't find that many of them, and I also would like to know if there is a reason as to why this is the case.
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Tight binding model calculation with Extended Huckel Approximation
I've been reading Albright's Orbital Interactions in Chemistry. In the chapter on solids, he provided a general approach to find the band structure of a solid state system
Now if we are to model a ...
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Evolutionary dynamics in vascularised tumors, PDE-ODE coupled system
I have to solve the following PDE-ODE system
$$ \displaystyle{\partial_{t} n = \bigl[a(s) - b(s)(y - h(s))^{2} - d\int_{\mathbb{R}} n \, dy \; + \; \beta \, \partial^2_{yy} n \;}
\\\\
\...
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How to handle system of chemical reactions for a batch reactor SciPy solver
I have a system of chemical reactions where the rate equations represent a batch reactor model. The model is a system of ODEs which is solved with the SciPy ...
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Getting started with Computational Chemistry
I´m now a chemistry grad student and I feel the need to get involved with computational chemistry and coding in the chemical field (in general). I have a very simple question: What is the best way to ...
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Maximize a function of an orthogonal matrix
I'm trying to write up a small code that, given a set of normal vibrational modes for a molecule, will convert them to localized vibrational modes. To do this I'm following the procedure from J. Chem. ...
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Software to simulate molten salt flow and thermodynamic operations
I was curious if there was any software (preferably in C++, Java, and/or python) that could be used to simulate the following:
Heat capacity of a fluid
Heat transfer through a liquid and a solid
...
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Non-linear flux interface condition - variational formulation
Context: I am working on implementing this paper and I am struggling to come up with a variational formulation for the Butler-Volmer interface conditions.
To simplify my question I consider the ...
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What determines the usual chemistry textbook plots of atom orbitals?
In elementary chemistry textbooks you often have pictures like the following one:
Are there any conventions how to get them?
I am not sure, but I guess that it are contour plots with only one iso-...
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What is the difference between ECPs and ADF frozen cores?
As the title suggests, what are the differences between the frozen core approximation as implemented by Amsterdam Density Functional and effective core potentials (ECPs)?
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Suggest methods and basis sets for a variety of systems [closed]
Please help me with any/all of the cases below. In the following cases, the named method and basis set are not suitable for the chemical systems. Why aren't they? Could you suggest a suitable method/...
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What equation should I fit this set of data points to?
I have done an experiment Estimation of silver nitrate by potentiometric titration with standard KCl solution.
A plot of $\dfrac{\Delta E}{\Delta V}$ versus Volume of KCl solution gives the ...
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What are the things I should keep in mind before doing an analysis of my gromacs simulation?
I did a liquid argon simulation at 100k. I forgot during analysis that I need to accommodate for the Periodic Boundary Conditions before doing any analysis which included distance. What are other such ...
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C++ library to mutate pdb residues
Are there any open source libraries available to mutate PDB protein residues? If so are do you have any examples of them?
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What is counterpoise correction?
What is counterpoise correction exactly ? Can you explain when it is needed and why ?
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Calculate activation energy of inter molecular displacement on a nano particle
I'm simulating a nano particle and wish to calculate the activation energy of the reaction where an atom is displaced from one point on the lattice to a neighboring void( might be at higher energy ...
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Oil/Water interface simulation using GROMACS
I would like to perform a decane/water(tip4p) interface simulation using GROMACS to analyse the fluctuation of the interface over a long period of time (50ps - 1ns).
Though I have a rough idea on ...
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Forcefield for studying a two phase system, consisting of noble gases and gaseous organic components
I am preparing to do a MD-simulation of a system which consists of two phases. The gaseous phase consists of $H_{2}$, $Ar$, $He$, $N_{2}$, $CH_{4}$ and $CO_{2}$. In this system, $p=0.355 ~bar$ and $T\...
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Parallelizing molecular simulation with full configuration energy
First, let just me stress that I'm not a an expert in computation chemistry, so now the problem:
We have GCMC molecular simulation, in the Grand Canonical ensemble, using the standard metropolis ...
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Quantum Chemical Calculations is there a book for which method to use with what problem?
Does anyone know of a book that will outline which quantum chemical methods are appropriate for what problems? I am trying to make informed choices before I start using computational resources. It is ...
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Solve rate equations with different reaction orders using SciPy ode
The image below illustrates the kinetic scheme I am trying to model.
My first example focuses on the conversion of the wood-oil to non-volatiles and volatiles. The rate equations are as follows:
$$
...
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What are alternatives to openbabel to convert CML file to image?
I recently started to perform natural resonance theory (NRT) analysis with NBO6. This program may automatically create a chemical markup language (cml) file with the treated structures. Unfortunately ...
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Is the Finite Volume Method conservative when the source term depends on the variable?
I trying to do a simulation where there are two quantities, $\Delta\theta(x,t) = \theta(x,t) - \theta_{o}$ and $\Delta\nu(x,t) = \nu(x,t) - \nu_{o}$. These quantities are chemical concentrations ...
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OpenFOAM precipitation/crystallisation reaction solver
This question is probably related to chemical engineers that are around this forum.
I am looking into writing a solver for a precipitation reaction (struvite to be precise): A+B+C+D <=> E+F
A, B, ...
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Gaussian and external basis set. How to write the input correctly [closed]
I have to use the LANL2DZpd basis set. It can be obtained from EMSL Basis Set Exchange.
But trying to calculate simple Me2Se molecule :
...
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DIIS method to accelerate SCF convergence for stretched geometries
I am implementing from scratch an Hartree-Fock calculation in the STO-3G basis set to perform Born-Oppenheimer molecular dynamics. I have a Restricted Hartree-Fock procedure that can reproduce very ...
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Borrow computational power from machines around me
I'm a computational chemist working with little computational power and dealing with increasingly demanding chemical systems. My work machines are part of a big network (mixed with windows and linux) ...
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