Questions tagged [computational-chemistry]
The branch of chemistry dealing with the use of mathematical models to solve problems in chemistry.
2
votes
2answers
89 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 ...
0
votes
0answers
34 views
Stochastic simulation Gillespie algorithm for areas instead of volumes?
I am trying to find resources on the Gillespie stochastic simulation algorithm for my system which happens on a surface. The original algorithm was developed for a reactor of volume $V$, but my system ...
1
vote
1answer
39 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 ...
2
votes
1answer
116 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 ...
1
vote
0answers
66 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
1answer
70 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 ...
1
vote
0answers
44 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
1answer
35 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
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0answers
49 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.
5
votes
1answer
2k 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:
$$
...
1
vote
0answers
142 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 ...
0
votes
3answers
102 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
1answer
899 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-...
3
votes
1answer
322 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 ...
7
votes
0answers
394 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
493 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 :
...
6
votes
2answers
890 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
vote
0answers
77 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) - \sqrt{n+1}\Phi_i^{*}\...
4
votes
1answer
273 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, ...
9
votes
0answers
108 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
71 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
28 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 ...
3
votes
1answer
778 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 ...
3
votes
1answer
78 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
218 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 ...
1
vote
0answers
103 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
618 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
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 ...
3
votes
1answer
261 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/...
3
votes
1answer
720 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
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 ...
1
vote
1answer
999 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} = ...
7
votes
1answer
7k 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 ...
2
votes
2answers
1k 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
262 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
199 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
123 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 ...
3
votes
2answers
101 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?
1
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0answers
483 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
134 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-...
16
votes
7answers
995 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
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 ...
7
votes
4answers
3k 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 ...
11
votes
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 ...
3
votes
1answer
536 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
votes
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 ...
5
votes
1answer
430 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
733 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 ...
10
votes
3answers
824 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 ...
8
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 ...
