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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Distance weighted interpolation

I got stuck while reviewing the journal article "Accurate reaction paths using a Hessian based predictor–corrector integrator". Why is the distance weighted interpolation done in the predictor steps, ...
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19 views

Potential energy Surfaces

I am trying to calculate PES for Molecular Oxygen and Atomic Nitrogen Exchange reaction. This is also known as Zeldowich reaction. I found that for asingle reactions, there are many PES's which I ...
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124 views

Why is MP2 failing to calculate proper IR frequencies for [Co(CO)4]^- and [Fe(CO)4]^{2-}?

I was doing some IR calculations on different 3d transition metal carbonyl complexes during some practical courses where we were introduced to effective core potentials. While doing this we found that ...
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65 views

Radical Computational Calculations [closed]

I am trying to calculate the total energies for a particular organic molecule that undergoes radical decomposition. I was able to calculate the neutral molecule with the exact results of a paper I ...
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3answers
140 views

Generating neat orbitals/surfaces from molden/wfn-files

I usually use Gaussian/GaussView and don't have to bother with other programs as I think that GaussView is capable of producing nice orbital/surface pictures like this one of one of uracil's ...
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29 views

calculate diffusion coefficient from MSD vs time [closed]

I have a trajectory file from simulation of 20,000 frames with 5 ps time in between every frame, what I want to do is to calculate diffusion in 2 dimension (x and y axis). but to calculate diffusion ...
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1answer
62 views

Carbohydrate configurations

I want to study several carbohydrates that includes but not limited to the following molecules: Glucose Galactose Mannose Fructose Tagatose Sorbose I know that for any carbohydrate, possible list ...
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3answers
195 views

InChIKey generation from InChI

I am trying to find some good resources to understand generation of InChIKeys from the InChI. There seems to be no resource available online. I have gone through the Wikipedia article for InChI, but ...
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43 views

What factors contribute most to solubility of ionic substances in highly polar solvents, esp. ionic liquids and DES?

I am trying to determine a method to dissolve a mineral salt with a lattice energy of ≈18000 kJ/mol. I know that lattice energy is the most significant factor affecting solubility of an ionic ...
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49 views

Free Web-Based Orbital Solver to look into the Walsh orbitals of a perturbed cyclopropane

There exists a free online orbital calculator. When I draw cyclopropane it plots three molecular orbitals, but unfortunately it doesn't use the Walsh orbitals. Are there any free online tools which ...
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39 views

Finding Ice CIF files in crystal database

Could anyone please tell me where I could find the the structure of cubic ice (ice Ic) as a .cif file? I have been searching the cambridge structural database using "H2O", "water", "dihyrogen oxide" ...
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89 views

Reliable automatic addition of hydrogens and charge assignment to small molecules at given pH?

I have some molecular PDB structures with missing hydrogens. Is there a software available that places missing hydrogens and assigns a charge to the molecule that is reliable? I have used Avogadro to ...
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1answer
122 views

How to read TINKER's force field parameters

I'm going to parameterize AMBER force field for the simulation of some small molecules. I have found the parameter sets provided by TINKER at here. I'm stuck here because I couldn't find any ...
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167 views

What happens if a polymer's length is equal to its persistence length?

So, I've been looking into polymer chemistry to model breaking polymers for a biological model, and I've been a bit stumped by the concept of persistence length. I know that if a polymer is ...
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1answer
96 views

What is GMEC (Global Minimum Energy Conformation)?

In a paper I have read the term GMEC, which was not further explained. GMEC stands for Global Minimum Energy Conformation. But what is it? Is it just the conformation with the lowest energy?
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34 views

Method of representing molecules as 3d objects with surfaces [closed]

I need a way of representing molecules in 3d form. I wish to be able to define a 3d surface for simple organic molecules. Can anyone advise me on this? Are there any approaches, or solutions to this ...
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2answers
84 views

Fitting parameters of Lennard-Jones potential to properties of real materials

I'm using the Lennard-Jones potential for some (very simple) protein docking simulation* and couldn't find parameters for different materials (like $\ce{C}$, $\ce{N}$, $\ce{O}$, …). Does it even make ...
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72 views

How to simulate surface tension?

I am trying to create a water drop simulation for measuring hydrophobicity of surface. I don't know how to simulate the contact angle which is related by younges equation to the surface tensions for ...
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3answers
100 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 ...
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134 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 ...
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89 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 ...
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1answer
218 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 ...
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120 views

How to interpret orbital transition in TDDFT?

Consider the following TDDFT run with GAMESS: ...
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188 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 ...
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54 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 ...
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1answer
87 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. ...
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1answer
120 views

How to interpret TD-DFT results for finding λmax 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 ...
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1answer
50 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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76 views

Are molecular optimizations in quantum chemistry really in vacuum?

I know that Gaussian (or other quantum chemical packages) assumes the molecule is alone in vacuum, that is, the molecule doesn't interact with anything, when optimizing the molecule. But I've found ...
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13 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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33 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. ...
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1answer
38 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 ...
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37 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
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1answer
82 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. ...
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60 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 ...
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196 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 ...
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2answers
80 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
70 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 ...
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1answer
155 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 ...
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1answer
68 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 ...
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2answers
252 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 ...
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2answers
96 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
36 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
70 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 ...
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1answer
81 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
62 views
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1answer
73 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
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1answer
243 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
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1answer
156 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 ...
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2answers
102 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 ...