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

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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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1answer
91 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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35 views

How to simulate a carbon nanotube in water using NAMD and VMD?

I am learning how to use NAMD and VMD to simulate carbon nanotubes. The NAMD tuturial does not provide examples of equilbrating nanotubes. Could someone one provide an example of nanotube in water? ...
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1answer
75 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
142 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 ...
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111 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 ...
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1answer
111 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
34 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 ...
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1answer
372 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
2k 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 ...
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2answers
143 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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1answer
99 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
88 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
111 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
155 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 ...
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1answer
105 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 ...
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7answers
754 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 ...
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1answer
68 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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4answers
781 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 ...
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4answers
712 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
201 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
526 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
332 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 ...
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2answers
414 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 ...
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3answers
504 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 ...
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4answers
1k 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 ...
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2answers
118 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 ...
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1answer
117 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)?
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2answers
860 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
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1answer
322 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 ...
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6answers
659 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 ...
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4answers
885 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 ?
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2answers
271 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). ...
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3answers
1k 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 ...
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3answers
2k 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 ...
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3answers
616 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 ?
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2answers
221 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 ?
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2answers
438 views

How to choose a basis set for ab-initio evaluations ?

How do I pick a basis set for an ab-initio Hartree-Fock evaluation ? In other words, what are the important characteristics of a basis set so that a proper choice can be made ?
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2answers
2k views

What is counterpoise correction?

What is counterpoise correction exactly ? Can you explain when it is needed and why ?
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3answers
302 views

Is Hartree-Fock always a good approximation for molecular geometries and no bond breaking ?

Are there cases where Hartree-Fock is not a good approximation to compute equilibrium geometry when the molecule is in a non bond-breaking condition?
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2answers
167 views

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

Can you explain the difference between these two computational methods ?