Questions tagged [computational-chemistry]
The branch of chemistry dealing with the use of mathematical models to solve problems in chemistry.
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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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pp.x command in quantum espresso
I am trying to generate the .pp and .cube file using pp.x -i (input file name) command. But, the .cube file is not getting generated and the output.log file also shows an error message.
this is my pp....
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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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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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Calculating radial distribution function in a cylindrical pore
I have tried calculating radial distribution functions in a cylindrical pore geometry. The pore has z-axis periodicity and it does not have x and y periodicity. But I got some troubles on that. The ...
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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 ...
user19247
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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 ...
user18279
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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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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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Time dependent self-consistent equations
I am facing the following problem. I need to solve numerically a set of coupled equations
$$i\frac{d}{dt}f_{n}^{(i)}(t) = \left[U\cdot n(n-1) + \mu\cdot n\right]f_{n}^{(i)}(t) - \sqrt{n+1}\Phi_i^{*}\...
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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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Are there any standardized file formats for point group character tables?
Character tables are an important tool for symmetry analysis in many computational chemistry software packages. Are there any standardized file formats for point group character tables?
This may seem ...
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Shifting points in fortran
Hello I am trying to shift points which have been previously generated in the square area. I am having a trouble with some additional conditions how they should have been shifted.
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Computational complexity of chemical dynamics for biological studies [closed]
How many CPU cycle is required to simulate a complete human body from it's very initial stem cell using classical algorithms and also is it possible to use similar algorithms for simulating stem cells ...
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Computer Build for Scientific Computing
I am currently a .NET software developer(SQL Server, ASP.NET, C#, MVC & Web Forms). In my spare time I'm researching different areas of environmental science. E.g.(Hydrology, Ecology, Atmospheric ...
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Is there any numerical application whose performance heavily depends on the division operation?
I am an undergraduate student majoring in computer science.
Recently, I am interested in the division operation, which is not directly supported by some architectures. While some architectures ...
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Global optimization methods in computational chemistry
I'm looking for a current and comprehensive overview (like a review article) of global optimization methods and their application in computational chemistry. Mostly I'm interested in geometry ...
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Center of Mass for molecule in Gaussian09
Gaussian09 prints coordinates where the local coordinate system as center at
$C = (\Sigma n_i*X_i)/(\Sigma n_i)$
where $n_i$ is the Mass Numer of the atom. However, the Mass Number is not actually ...
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Installing GPAW (Python DFT package) on a computing cluster
I'm in the middle of installing GPAW on a cluster but I'm running into problems building the "gpaw-python" interpreter, its job is to allow users to execute parallelised GPAW calculations. Following ...
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