Questions tagged [computational-chemistry]

The branch of chemistry dealing with the use of mathematical models to solve problems in chemistry.

Filter by
Sorted by
Tagged with
2 votes
1 answer
140 views

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. ...
2 votes
0 answers
107 views

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\...
2 votes
2 answers
165 views

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 ...
4 votes
2 answers
404 views

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 ...
0 votes
0 answers
108 views

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....
1 vote
1 answer
333 views

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 ...
40 votes
23 answers
10k views

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 ...
1 vote
0 answers
45 views

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 ...
0 votes
0 answers
193 views

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 ...
-1 votes
1 answer
66 views

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 ...
2 votes
0 answers
45 views

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 ...
0 votes
1 answer
1k views

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).
2 votes
1 answer
107 views

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 ...
0 votes
0 answers
77 views

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 ...
7 votes
2 answers
401 views

What is the difference between Coupled Cluster SD and SD(T)?

Can you explain the difference between these two computational methods ?
20 votes
6 answers
7k views

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 ...
6 votes
4 answers
1k views

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 ...
9 votes
1 answer
10k views

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 ...
0 votes
0 answers
43 views

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 ...
0 votes
0 answers
57 views

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 ...
2 votes
1 answer
249 views

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?
7 votes
5 answers
7k views

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 ?
1 vote
0 answers
33 views

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, ...
10 votes
2 answers
2k views

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 ?
0 votes
1 answer
136 views

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.
1 vote
0 answers
117 views

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 ...
5 votes
0 answers
101 views

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 \;} \\\\ \...
0 votes
0 answers
219 views

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 ...
1 vote
1 answer
3k views

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 ...
5 votes
3 answers
721 views

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. ...
0 votes
1 answer
136 views

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 ...
3 votes
1 answer
203 views

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 ...
5 votes
1 answer
1k views

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-...
4 votes
1 answer
303 views

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)?
3 votes
1 answer
325 views

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/...
2 votes
2 answers
692 views

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 ...
1 vote
1 answer
65 views

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 ...
3 votes
2 answers
144 views

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?
16 votes
2 answers
11k views

What is counterpoise correction?

What is counterpoise correction exactly ? Can you explain when it is needed and why ?
2 votes
0 answers
92 views

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 ...
1 vote
1 answer
260 views

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 ...
0 votes
1 answer
60 views

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\...
1 vote
0 answers
67 views

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 ...
0 votes
3 answers
182 views

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 ...
5 votes
1 answer
5k views

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: $$ ...
2 votes
0 answers
404 views

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 ...
2 votes
1 answer
1k views

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 ...
4 votes
1 answer
435 views

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, ...
-1 votes
1 answer
1k views

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 : ...
8 votes
0 answers
577 views

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 ...