Questions tagged [computational-chemistry]

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

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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 to call an analogous limiting reagent?

I'm trying to find either an Excel function or some other calculator that will tell me the number of possible complete combinations/sets of an item given amounts of components. I'm a high school ...
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2answers
108 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 ...
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1answer
43 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 ...
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1answer
150 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 ...
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0answers
76 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 ...
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1answer
83 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 ...
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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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1answer
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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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217 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 ...
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3answers
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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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1answer
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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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1answer
381 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 ...
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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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602 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 : ...
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2answers
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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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1answer
292 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, ...
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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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1answer
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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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1answer
30 views

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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1answer
946 views

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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1answer
253 views

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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114 views

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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1answer
716 views

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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1answer
115 views

Optimizing MPICH2 on FX 9370 processor

Short version of question: We have a Opteron 6272 cluster, an we have recently started bilding FX 9370 based small cluster. Problem is that we are not able to get desired speed, i.e scaling with ...
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1answer
269 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/...
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1answer
771 views

Molecular dynamics: how to calculate interfacial tension [closed]

How can one determine the interfacial tension at a solid-liquid interface using molecular dynamics? What are some good articles on this topic?
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2answers
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Quantum chemistry - are there potential issues to be concered about when using mixed basis sets in a calculation?

I'm attempting to model energies of a transition metal complex using hybrid DFT but having issues with the description of my metal centers. The problem is alleviated by adding extra polarization ...
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1answer
1k views

Implicit heat diffusion with kinetic reactions

I am using the implicit finite difference method to discretize the 1-D transient heat diffusion equation for solid spherical and cylindrical shapes: $$ \frac{1}{\alpha}\frac{\partial T}{\partial t} = ...
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1answer
8k 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 ...
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2answers
2k views

Does energy decrease with basis set size in density functional theory?

Based on the variational principle, one might expect that the ground state energy of a density functional theory (DFT) calculation will decrease as the basis set size increases. (As I understand it, ...
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275 views

nudged elastic band with Turbomole

Is there any free / open source solution to search for the minimum energy path with the nudged elastic band method in combination with the Turbomole Package?
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1answer
203 views

How to manipulate dihedral angles in pre-optimized molecule coordinates?

I want to explore the low energy states of an amino acid or a peptide by generating input geometries, defined by multiple dihedral angles of the backbone or the side chain. From these starting ...
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1answer
125 views

Trying to generate a wave function basis set

For a little project I'm working on, I am trying to generate a wavefunction basis set I can use in Quantum Monte Carlo (DMC to be specific). Preferably, it would be a linear combination of Slater ...
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2answers
116 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?
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1answer
137 views

Calculating AIC (in R or any other statistical software)

I am trying to fit the log-log plot of the cumulative distribution of a network to one of three models: Exponential (EXP) ($P(k)\sim e^{-ak}$), Exponentially truncated power law (TRU) ($P(k)\sim k^{a-...
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7answers
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Does Computational Science involve programming?

I read about computational science on Wikipedia, but my understanding is not very clear. Does computational science involve programming? How different is computational science from computational ...
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1answer
70 views

Thermoplastic Equation solving

I was given a problem by my professor as follows Solve the System $pV=S$ $pcT=kT+BS\frac{dG}{dt}$ $\frac{dS}{dt}=\mu(V-\frac{dG}{dt})$ $\frac{dG}{dt}=f(S,T)$ Where $p$, $c$, $B$, $\mu$ are ...
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Best hardware solution for microsecond Molecular Dynamics

We would like to reach Molecular Dynamics simulation of proteins with around 20000 atoms in explicit water with trajectories of around 1 microsecond each. We are looking at different options for ...
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4answers
1k views

good (free) software for producing publishable images?

I am producing 1d and 2d images using Matlab right now for comparison of accuracy against a given model. I need to compare my methods with the standard Gaussian .wfn model and I am going to do that by ...
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1answer
616 views

In molecular dynamics (MD) simulations, how is particle number density computed in practice?

I have been reading a recent paper. In it, the authors performed molecular dynamics (MD) simulations of parallel-plate supercapacitors, in which liquid resides between the parallel-plate electrodes. ...
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4answers
1k views

Making a Molecular editor/visualizer: Object oriented programming, data structures, and molecules

I am new to programming and I am trying to solve my first big problem and write my first big program. I have looked for open source examples of code to learn from, but so far have only found code in ...
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1answer
445 views

Implementing simple atom model using density functional theory (DFT)

I am trying to write computer code which will find the energy and density function for a atom with Z protons and N electrons. I am working in 1D for simplicity and would like to make the overall code ...