Questions tagged [computational-chemistry]
The branch of chemistry dealing with the use of mathematical models to solve problems in chemistry.
75
questions
6
votes
4answers
923 views
How important is learning hardware/architecture for scientific computing?
Apologies if this is a bit of a soft, unclear, or opinion-based question. I'm a relatively new PhD student in a (computational) quantum chemistry group. My group develops and maintains a few software ...
0
votes
0answers
41 views
Reference request: Textbook similar in structure to "Computational Materials Science: An Introduction" by June Lee for Computational Biology
In the Computational Materials Science: An Introduction by June Lee, he discusses molecular dynamics and density functional theory with examples from LAMMPS and QuantumEspresso, and explains LAMMPS ...
0
votes
0answers
45 views
Moller Plesset Theory- MP2 correction
I have a molecule LiBH2 with C2V point group. I used 3-21G basis set and obtained RHF coefficients and symmetry of orbitals. I wish to find the set of orbitals (a,b,i,j)( where a and b are occupied ...
2
votes
1answer
141 views
Applications of Julia in Chemistry and Molecular Physics?
I was wondering if there are any Theoretical & Computational Chemistry (MM, QM) codes or publications out there that are based primarily on the Julia programming language?
1
vote
0answers
30 views
Why is scoring a separate problem even after docking is done?
With regards to protein-ligand interactions, we talk about two concepts, docking and scoring. I understand that docking means to find the best orientation of a ligand at the active site of a protein, ...
1
vote
0answers
76 views
Tight binding model calculation with Extended Huckel Approximation
I've been reading Albright's Orbital Interactions in Chemistry. In the chapter on solids, he provided a general approach to find the band structure of a solid state system
Now if we are to model a ...
5
votes
0answers
91 views
Evolutionary dynamics in vascularised tumors, PDE-ODE coupled system
I have to solve the following PDE-ODE system
$$ \displaystyle{\partial_{t} n = \bigl[a(s) - b(s)(y - h(s))^{2} - d\int_{\mathbb{R}} n \, dy \; + \; \beta \, \partial^2_{yy} n \;}
\\\\
\...
0
votes
0answers
73 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 ...
1
vote
1answer
2k 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 ...
5
votes
3answers
373 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. ...
0
votes
1answer
109 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
...
37
votes
18answers
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 ...
2
votes
2answers
511 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 ...
1
vote
1answer
55 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 ...
3
votes
1answer
188 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 ...
2
votes
0answers
91 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
164 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
61 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
54 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\...
0
votes
1answer
122 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
4k 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
347 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
157 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
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-...
2
votes
1answer
674 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 ...
8
votes
0answers
544 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
1k 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
1k 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
94 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
366 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, ...
11
votes
0answers
134 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
82 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
31 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
2k 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
80 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
289 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
291 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
808 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
126 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
301 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
931 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?
2
votes
2answers
53 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 ...
3
votes
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} = ...
9
votes
1answer
10k 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 ...
3
votes
2answers
3k 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
339 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
231 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
131 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
136 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
vote
1answer
138 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-...
