We’re rewarding the question askers & reputations are being recalculated! Read more.

# Questions tagged [computational-chemistry]

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

69 questions
Filter by
Sorted by
Tagged with
13 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 ...
74 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 ...
96 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. ...
74 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 ...
152 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 ...
9k 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 ...
14 views

### 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 ...
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-...
232 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)?
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/...
111 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 ...
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 ...
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?
7k views

### What is counterpoise correction?

What is counterpoise correction exactly ? Can you explain when it is needed and why ?
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 ...
84 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 ...
38 views

48 views

### 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 ...
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, ...
115 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 ...
725 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 ...
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 ...
906 views

### Why does iteratively solving the Hartree-Fock equations result in convergence?

In the Hartree-Fock self-consistent field method of solving the time-independent electronic Schroedinger equation, we seek to minimize the ground state energy, $E_{0}$, of a system of electrons in an ...
126 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 ...