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

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30 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 ...
0
votes
0answers
30 views

Adding a new potential term to DL_POLY Classic

I am using DL_POLY Classic to simulate CO2 behavior in upper mantle conditions. I am trying to use a recently new forcefield for this system. In this FF, the potential energy between two atoms in the ...
7
votes
0answers
43 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 ...
-1
votes
1answer
29 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 : ...
4
votes
3answers
133 views

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) ...
1
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0answers
43 views

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) - ...
-1
votes
1answer
64 views

The thermodynamic affinity [closed]

I try to validate the results of an hypersonic one-dimensional air flow behind a strong normal shock wave, particularly, the relaxation distance. I get a distance of ~ 30 cm ( for $M_\infty$ = 25, ...
4
votes
1answer
127 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, ...
8
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0answers
75 views

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 ...
1
vote
1answer
63 views

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. ...
1
vote
1answer
24 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 ...
1
vote
1answer
124 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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0answers
38 views

How to read gamess output files

I have worked Gaussian for a long time and used subroutines to read .wfn files and return the Electron Density. Are there any open source functions or subroutines ...
3
votes
1answer
76 views

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 ...
2
votes
1answer
101 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 ...
0
votes
0answers
50 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 ...
2
votes
1answer
258 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 ...
2
votes
1answer
109 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 ...
3
votes
1answer
196 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 ...
0
votes
0answers
143 views

How can we visualize the data in polar coordinates using openDx?

Actually I am trying to visualize data in polar coordinates using openDx but openDx always does in Cartesian coordinates i-e in box shape I want circular shape of my data. I want the data ...
3
votes
1answer
243 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?
1
vote
2answers
38 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 ...
0
votes
1answer
650 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} = ...
6
votes
1answer
4k 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 ...
2
votes
2answers
388 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, ...
0
votes
1answer
154 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?
1
vote
1answer
144 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 ...
2
votes
1answer
116 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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0answers
246 views

Extracting geometry data from Gaussian09 geometry optimization

I want to extract the geometry for every single step of a Gaussian09 optimization from the .log file. I need the results in cartesian XYZ format, either in one file or in multiple files. First I ...
1
vote
1answer
120 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 ...
14
votes
7answers
849 views

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 ...
0
votes
1answer
69 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 ...
5
votes
4answers
2k views

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 ...
12
votes
4answers
966 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 ...
2
votes
1answer
266 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. ...
11
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4answers
766 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 ...
5
votes
1answer
370 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 ...
12
votes
2answers
565 views

How can one mathematically describe the “cartoon” type of representation of proteins?

Proteins are typically represented in a cartoon form, with β sheets as arrows and α helices as coils: I'm wondering, is there somewhere a reference that describes the construction of this ...
8
votes
3answers
609 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 ...
7
votes
4answers
2k views

Are open-source codes available to study protein folding?

I would like to test the influence of solvation parameters in implicit solvation models and wonder which codes are freely available as standalone programs for protein folding of small proteins, and ...
7
votes
2answers
133 views

Can quantum methods be applied to the protein-ligand docking problem?

In the problem of protein-ligand docking, most of the time people are happy if they can just predict the final conformation the ligand adopts into the protein's binding pocket. Most of the time one ...
3
votes
1answer
141 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)?
2
votes
2answers
1k views

How does Gaussian 09 handle 'Frozen Core Approximations' and how does it compare to CFour handling?

Background I'm currently working with two quantum software packages: Gaussian 09 and CFour. CFour does a very good job giving explicit control over how you want to invoke frozen core approximations ...
12
votes
1answer
326 views

Enumeration of graphs deriving from Delaunay tessellations in 3D

Is there an algorithm that enumerates the graphs that correspond to some Delaunay tessellation of points in 3D? If so, is there an efficient parameterization of geometries that correspond to any ...
10
votes
6answers
904 views

What open source tools are available to visualize molecular vibrations?

I would like to visualize a molecular vibration that is not a normal mode. I'd like to present a static, vectorial representation of the motion, and I would like some flexibility in the vector style ...
5
votes
4answers
2k 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 ?
5
votes
2answers
309 views

Pauli repulsion contribution in electronic structure computations

I am looking for a method to estimate the contribution from Pauli repulsion to the interaction energy of a molecular dimer in an electronic structure computation (e.g. with Density Functional Theory). ...
15
votes
6answers
2k 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 ...
11
votes
3answers
3k views

How is B3LYP implemented in Gaussin 0*, GAMESS-US, Molpro, … etc?

Specifically I want to extend work involving B3LYP started with Gaussian 03 but continued with GAMESS-US. The energies provided by the default B3LYP methods are not the same. There is a discussion ...
2
votes
3answers
1k views

Differences between Gaussian and Slater functions on the quality of the results?

Given two computational programs, one using a Gaussian basis, and the other using Slater basis, what are the practical differences, advantages and disadvantages for each choice ?