A field which implements computers to model and study chemical systems and chemical behavior, usually by approximating the Schrodinger equation for a given chemical system.

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54 views

Is it wise to use ECPs on light atoms for electronic structure calculations?

So, I have a big organic molecule consisting of $\ce{H}$, $\ce{C}$, $\ce{O}$, and $\ce{N}$ atoms and the goal is to find its equilibrium geometry and US/Vis spectrum. The molecule is so big that I was ...
5
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1answer
101 views

What is the exact meaning of GAMESS (US) SCF density convergence criteria?

In Gaussian the SCF convergence criteria is set to $10^{-N}$ by SCF=(Conver=N) Note that this criteria applies to the root mean square change in density matrix ...
2
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2answers
64 views

How would you add saccharide residue information to PDB files?

I have multiple PDB files containing a single molecules of polysaccharides, with a single chain and a long list of all the atoms -they are not divided by residue. The PDB files were created from ...
5
votes
1answer
172 views

What is GAMESS and Gaussian?

I've been seeing a lot of GAMESS and Gaussian questions around here, and most of them seem very hard to answer. I extrapolated that they might be some sort of Chemistry programs, but what do they do ...
3
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2answers
62 views

How to interpret orbital transition in TDDFT?

Consider the following TDDFT run with GAMESS: ...
9
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2answers
173 views

Why Acetone does not behave like its computational values?

I am trying to simulate the excitation state of acetone. I ran TDDFT for it both in gas phase and solvated state in water (both implicit and explicit water). The experimental data say that acetone ...
4
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0answers
42 views

Andersen thermostat in MD with rigid bond constraints

I have been writing a custom MD code for some time. I have been using the andersen thermostat, mainly because its ease of use, and the fact that I am not concerned with gathering dynamical data, but ...
3
votes
1answer
43 views

How to calculate molecular dipole moment from a known wavefunction?

Say I have a molecular wavefunction as a set of molecular orbitals and want to calculate the molecule's dipole moment, but don't know how ! I searched a lot but couldn't find any practical example. ...
3
votes
1answer
100 views

How to interpret TD-DFT results for finding ╬╗max and amplitude

I am trying to understand how to interpret the TDDFT results ( I know there is another post for this but it does not answer my question ). Here is part of the result from GAMESS: I downloaded ...
5
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1answer
44 views

What program could I use to create a protein model from scratch?

I would like to create protein models such as the ones in the Protein Data Bank. I have got GROMACS but I don't know if it can be used to model macromolecules.
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0answers
24 views

Dissociation Energy for CO2 per molecule

I'm trying to calculate the energy required to dissociate a single $\ce{CO_{2}}$ molecule into its respective elements, and I'm given that it takes $ 373.6 \times 10^{3} \, \, \frac{joules}{gram} $ ...
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1answer
24 views

Are molecular optimisations in Gaussian really the optimisations of molecules in vacuum?

I knew that Gaussian assumes the molecule is alone in vacuum, that is, the molecule doesn't interact with anything, when optimising the molecule. But I've found that Gaussian's optimisation(at HF or ...
2
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0answers
12 views

Merge rigid parts and flexible results after docking (Vina)

If I use flexible residues in the binding pocket, they are cut from the file. The protein is broken and the amino acids are unbound in the room. How can I get my results and the protein together ...
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0answers
16 views

Autodock Vina flexible metals and water molecules

I have some problems with water and metals in binding site when using Autodock Vina. Is it possible to make these flexible? They unfortunately remain where they are what leads to wrong interactions. ...
4
votes
1answer
36 views

Charge consistency in fragment qm/mm methods

I'm calculating the multipole moments on several fragments of a molecule. What are some procedures to ensure that the charges etc are representative of the complete molecule? How do I ensure I'm not ...
1
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0answers
25 views

Basis set in the computational software “Gaussian-03” for studying adsorption of a hydrogen atom on a carbon paste electrode dropcasted with Pt-CNT

What is the basis set in the computational software "Gaussian-03" that can be used to study the interaction of $\ce{H}$-atom with $\ce{Pt-CNT}$ dropcasted electrode? How can we study the energy ...
3
votes
1answer
45 views

Most efficient level of theory for sulphur-containing proline analogues (one that will work)

I'm modelling a small set of proline analogues - extra functional groups, sulphur in the ring. Using Gaussian / DMACRYS. ...
5
votes
1answer
55 views

Viewing a protein or bio structure in Chembio3D in its natural conformation

I notice when using SMILES or a IUPAC name for many molecules and generating them in Chembio3D, and then running MM2 > Minimize Energy, the structures produced are most of the time not reflections of ...
8
votes
3answers
178 views

How to define custom force in quantum chemistry packages?

I dont know if this is really applicable but I want to add a custom force ( say F(x,y,z) ) to some atoms in my geometry optimization. Is there any way to add such forces to the DFT or Molecular ...
3
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2answers
45 views

Gaussian Convergence Issue for N2+N PES

I am trying to obtain a potential energy surface (PES) for $\ce{N2 + N}$ combination using scan feature of Gaussian. I have tried different combinations of basis ...
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1answer
48 views

How to extract wavefunction from GAMESS output?

Is there a way to extract the molecular wavefunction from GAMESS output? I know there are packages that can extract the eigenvalues or the exponents and show them as a table but that is not of much ...
4
votes
1answer
146 views

Usefulness of the outdated Bohr model?

Whilst the Bohr model is incomplete and incorrect, it had limited usage in predicting spectral lines. In the same way, could it possibly with limited accuracy, be used to predict the outcome of ...
1
vote
1answer
56 views

Computational Chemistry (Ab Initio), what should I study?

I am interested in ab initio computational chemistry.I am trying to figure out what I should study. I know that I should study physical chemistry, mathematics, and programming. However, I am not sure ...
3
votes
2answers
212 views

How to calculate molecular volume from the wavefunction?

Very short question but maybe not a short answer ! As the probability of presence of electrons in a specific spatial position is defined as square of the wave function, I am wondering if there is a ...
4
votes
2answers
94 views

How to calculate vibrational spectra of organic molecules?

I watched a ted talk (Luca Turin: The science of scent) and was wondering if anyone had any examples of how to calculate vibrational spectra of molecules (used as fragrances)? Would love to figure ...
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1answer
29 views

short/extensive training on computational chemistry [closed]

I want to take a training on computational works in chemistry. It should be of a short duration. Where in Europe I can find it?
2
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1answer
49 views

How to get a protein's dihedral angles ordered by variance?

The setting: I want to simulate protein docking and let some dihedral angles vary, but in order to keep it low-dimensional I have to select those which are most likely to change. What I've thought of ...
0
votes
1answer
64 views

Is there a way to efficiently estimate the enthalpy of formation for an organic molecule in computational chemistry?

I'm exploring the platonic hydrocarbons and one of the methods I'd like to use is to compare their enthalpies of formation. The issue is that carbon's standard form is a covalent lattice and I can't ...
4
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1answer
57 views
4
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1answer
64 views

Why are C6 dispersion forces named C6?

I'm reading about water models and their dispersion coefficients, and going back to S. C. Wang's work according to the citation of an equation (Google books here) As you can see one citation's to a ...
2
votes
1answer
183 views

Which is most reliable excitation energy: LUMO-HOMO energy or TD-DFT excitation energies?

After running a TD-DFT , we can calculate the HOMO-LUMO difference and then calculate the the excitation energy. Another approach is just simply pick the energies calculated in the TD-DFT and use ...
7
votes
1answer
131 views

GAMESS and Gaussian : what is the maximum efficient number of supported nodes?

I have looked at GAMESS and Gaussian manuals but can not find the maximum number of efficient nodes. As I tried GAMESS on our supercomputer, I can add as many CPUs as I want but it really does not ...
2
votes
2answers
67 views

How to find molecular charge of fragments using quantum calculations?

Assume in a software like Avogadro, I put molecules A and B in a specific distance and I know they will involve in a charge transfer reaction ( as Marcus Theory outer sphere transfer ). Then I run a ...
10
votes
4answers
342 views

DFT Functional Selection Criteria

I have a very very general question: In DFT functional selection , mostly people speak about the most recent ones. For example my professor always asks: " which DFT Functional did you select ? " ...
2
votes
1answer
48 views

How to run crystal simulation on GAMESS?

I know GAMESS is not best suited for crystal simulation but I am not ready to start learning another package as VASP. As I heard GAMESS is able to do some calculations in a "terminated" crystal (I ...
3
votes
1answer
102 views

How can you manage SCF convergence problems?

"Failure to locate stationary point, SCF has not coverged" This is the most annoying message after Optimization run ( even with a good primary start geometry like UFF we ay see that) . The only ...
2
votes
2answers
71 views

Molecular Assembly Program

I'm not totally sure which Stack Exchange community this would go in, but Chemistry seemed best. I've been thinking for a long time now, that it would be cool to have a program where you could design ...
2
votes
1answer
176 views

How to Run GAMESS and Avogadro on Command Line?

I always use GAMESS and Avogadro on my own laptop. Recently I installed them on our university supercomputer and started using them by remote logging-in. On the laptop everything was super easy but ...
4
votes
1answer
81 views

Post-Hartree Fock Methods

I'm new to computational chemistry, so perhaps this question has an obvious answer. I'm wondering what the intuitive reason for constructing Slater determinants that involve excited states is, when ...
8
votes
2answers
353 views

Does chemistry need machine learning?

In many fields of science (e.g. biology, medicine, psychology, statistics, physics), machine learning and artificial intelligence techniques are becoming more and more popular to analyze data. Is it ...
2
votes
1answer
21 views

Oxide surfaces develop a charge in H2O. Do we have any, even vague, handle on how long does an indivdual charge last on avg. before being neutralised?

We often know, from e.g. titration experiments, what the average surface charge density of a surface is. How do these charges vary over both time and space (i.e. dynamics)? I have been unable to find ...
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5answers
4k views

Why is FORTRAN so commonly used in computational chemistry?

I've been using Ruby to write scripts for research, but I want to get into some heavier stuff that Ruby is just too slow for. I noticed there are a few things written in C and C++, but there is an ...
2
votes
1answer
130 views

What tools can be used to estimate binding energies?

I want to estimate the binding energies of various molecules. What are the analytical and numerical tools I can use for this purpose? In particular I'm interested in bonding energies of dyes to ...
5
votes
3answers
70 views

Intrinsic Reaction Coordinate calculation— both sides of TS lead to same minimum

I am currently trying to find an addition transition state and verify it using an IRC calculation. I have found a good candidate, but the IRC calculation gives the same minimum on each side of the ...
3
votes
2answers
89 views

Any popular experiment in chemistry that digital signal processing played a crucial role in?

Is there any famous experiment in chemistry where digital signal processing played an important part? I don't mean using a machine that relies on such techniques (they all do) but an experiment where ...
2
votes
2answers
47 views

What's the reason for discrepancy between DFT calculated image and NC-AFM-acquired one in this article?

Looking at the images in this article, I've noticed that the molecule electron density images showed as calculated via DFT look very symmetric, while those obtained by NC-AFM appear somewhat ...
1
vote
1answer
61 views

How to calculate a reaction's DeltaH using a MM forcefield calculator software?

I want to calculate $\Delta H$ for hydrogenation of Benzene and producing Cyclohexane using MM+ Force Field Energy. I am using Hyperchem for energy calculation and optimization. I calculated the ...
7
votes
2answers
75 views

Quick-and-Dirty Molecular Dynamics by Mass-Weighted Atom Translations?

I'm thinking about a quick-and-dirty approach to molecular dynamics, mostly for teaching purposes. At a given temperature, statistical mechanics tells us molecules have translational and rotational ...
0
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0answers
18 views

Carbonation process - Equation in Mathlab

I need some help with the Carbonation process of how soda/fizz water is produced. I just found the equation, but I do not know how to model the process in Mathlab. Can anybody advise me with some ...
3
votes
1answer
74 views

Unitary Transformation of the HF equations

I am working on a code to preform a HF procedure and I am a bit confused about the unitary transformation of the basis. My instructions are as follows. specify the basis and geometry (done) ...