Questions tagged [potential-energy-surface]

Questions about potentiology.

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A good 2D function for plotting and visual demonstration of transition state, reaction coordinate etc

I am looking for a nice 2D function which has two minima and one saddle point, and ideally a curved reaction path which I can use to draw contour plots on matplotlib. I will use these contour plots in ...
S R Maiti's user avatar
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2 votes
1 answer
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Si Thin film phonon dispersion with negative frequency

I have a Si slab of thickness 0.5nm for which I want to calculate the phonon dispersion. The unitcell has 5 atomic layers and 10 Si atoms with vacuum of 10A in z-direction (a 2x2 supercell is shown ...
Mohamed Saleh's user avatar
2 votes
0 answers
22 views

Are there any good tutorials on SHARC-Gaussian interface?

I am an aspiring quantum chemist planning on trying out the SHARC approach to study excited state proton transfer dynamics of organic molecules. I am comfortable with Gaussian 16 as that is the ...
Uranium238's user avatar
2 votes
0 answers
20 views

How to seperate structures in bulk with connectivity from a relaxed scan in Gaussian 16?

I aim is to construct the PES for a molecule considering a specific bond length as the scan coordinate. I am using the Relaxed-Scan feature of Gaussian 16 for this using the ...
Uranium238's user avatar
4 votes
1 answer
70 views

How do I do a PES (potential energy surface) scan for the excited electronic state?

I know how to do a PES scan for a ground electronic state. But for the nth-excited state, is it the same (i.e. an excited state optimization and just rotating the dihedral to simulate the ...
WALOWLA's user avatar
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5 votes
2 answers
244 views

Gaussian 16: Relaxed scan using Jacobi coordinates expressed using generalized internal coordinates

For teaching porpouses, I would like to make a relaxed scan for an A-BC system (for example, the isomerization of of H-NC to H-CN or CH3-NC to CH3-CN) with Gaussian 16 using generalized internal ...
PAEP's user avatar
  • 195
6 votes
2 answers
107 views

What is the branching space of a conical section?

I am currently engaged in reading a research paper that focuses on the computation of the Potential Energy Surfaces (PES) of excited states. Within this paper, there is a discussion about a concept ...
Paulie Bao's user avatar
  • 3,953
6 votes
1 answer
144 views

Do conformations arise from vibrations?

Cross-posted on Chemistry SE. I was wondering how a molecule transforms from one conformation into another. Surely, since the conformations are separated by a potential barrier, some activation energy ...
ananta's user avatar
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3 votes
0 answers
136 views

Advise in generating ESP surfaces from Gaussian .cube files using the IQmol software

I am trying to generate an ESP surface of a Gaussian09 calculation using the iqmol software. I have used Gaussview to visualize the ESP surface by generating .cube files from .fchk files (using the ...
Kevin Freddo's user avatar
3 votes
1 answer
65 views

What is the gold standard ab initio pair-potential between two water molecules?

There are a myriad of pair potentials available for simulating the interactions between water molecules, ranging from simpler models like the SPC/E to more sophisticated ones based on high-level ...
Lodin Ellingsen's user avatar
5 votes
1 answer
77 views

Using Hindered Rotor Scans With Different Convergence Criteria from Gaussian

I am having trouble with a difficult convergence in Gaussian16. I am running two separate PES scans for hindered rotors in my molecule that will eventually be used in subsequent rate calculations. I ...
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3 votes
1 answer
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Potential Energy curve for CO2 and a surface

I am trying to calculate the potential energy curve for the interaction between CO2 and a silica surface. I use 3 systems and run single point calculations with LAMMPS and substract the values like E =...
Xdrake's user avatar
  • 541
3 votes
1 answer
163 views

Script to draw one-dimensional PES comparing harmonic and anharmonic vibrational modes

This is an extension of a question I asked a little while ago: Software to draw one-dimensional PES including vibrational energy levels. I am asking the followup here based on advice received after ...
isolated matrix's user avatar
3 votes
1 answer
358 views

What is the difference between actual energy vs scf energy in an orca scan

Always at the end of the output of a scan type calculation in orca there are two tables one with the name "The Surface Calculated using the 'Actual Energy'" and the other "The Surface ...
Mateus Augusto's user avatar
6 votes
1 answer
114 views

Slope of the potential when both molecules "touch"?

My aim is to model the potential energy surface for two colliding H2 molecules. More specifically, I needed the order of magnitude of the slope of the potential at the moment when two colliding H2 ...
More Anonymous's user avatar
3 votes
1 answer
222 views

Is the energy due to external electric field included in gromacs energy?

I have a Gromacs NVT simulation with a constant external electric field using the option "electric-field-z = 1.5 0 0 0". When calling gmx energy -f (...).edr to calculate the potential ...
curio's user avatar
  • 131
6 votes
1 answer
141 views

Are there any available tools to implement Jellium models?

I want to solve a Jellium-DFT like problem. Does any of the self-consistent/DFT software packages available allow to solve for the case of a Jellium configuration (no lattice)? If not I would like to ...
Jellium mind's user avatar
7 votes
2 answers
763 views

Parameterising a Lennard-Jones interaction: Which atoms should I scan to build potential energy surface?

I have a question related to parameterize Lennard-Jones interaction to get sigma $\sigma$ and epsilon $\epsilon$ to include in amber force field to do the Molecular Dynamics. I searched a lot, they ...
Abd-Elazeem Mohamed's user avatar
8 votes
1 answer
708 views

Restart potential energy scan in Gaussian with additional scan points

I have finished a scan of a bond length, but I need to continue the coordinate scan adding more points to the same scan. I thought of writing a second input file from the last geometry, relaunching ...
Andrea Pellegrini's user avatar
9 votes
2 answers
711 views

Is it reasonable to calculate TDDFT excitation energies at a geometry optimized with a different method?

I am working on a project where I have to calculate the TDDFT excitation energies of organic molecules (to compare to the experimental UV/visible i.e. optical absorption spectrum). Now, if I ...
S R Maiti's user avatar
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5 votes
1 answer
173 views

Software for generating ensembles of dimer pairs of organic molecules

For two organic molecules of essentially unlimited size (up to and including, and sometimes exceeding MW = 1000 g/mol), I would like to generate all possible dimer pairs in vacuum. The pairs may be ...
Wesley's user avatar
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5 votes
1 answer
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What is the equilibrium bond length for a Lennard-Jones potential?

If I have $\epsilon$ and $\sigma$ can I calculate equilibrium distance $r_e$ in one run? What I have tried is to put $V = \epsilon$ and bring out the $r$ from the formula, but it seems not solvable. ...
John T's user avatar
  • 666
10 votes
2 answers
2k views

Is it possible to do a Gaussian redundant scan with some fixed bonds?

I'm trying to do a redundant PES scan of a hydrogen abstraction in a Gaussian job while maintaining the rest of the system fixed. I need to scan the coordinate where H5 approaches to H6, maintaining ...
christian's user avatar
  • 103
8 votes
1 answer
71 views

PES of Tetramethylthiuramdisulfid / Problem with Disulfidbridge

I like to perform a DFT Study on Tetramethylthiuramdisulfid. So I made a structure optimization for my start structur with PW6B95D3/aug-cc-pvtz to get a good structure to begin my dihedral scan to get ...
Andrea's user avatar
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9 votes
3 answers
532 views

What is the procedure for constructing an ab initio potential energy surface for CH3Cl + Ar?

I would like to construct a model analytical potential function for collision between CH3Cl and Ar. This would be the sum of CH3Cl intramolecular + CH3Cl---Ar intermolecular potential. First I would ...
fred85's user avatar
  • 99
10 votes
1 answer
497 views

How to create a Potential Energy Surface in Chemcraft?

The Chemcraft website says that it is possible to create a potential energy surface. Nevertheless, it doesn't work for my Gaussian scan job. ...
Till's user avatar
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11 votes
2 answers
143 views

What are some available software packages for automated finding of local and absolute minima on PES?

I have never used any AI driven calculation package before and to be honest don't fully understand the ins and outs of it. To be more specific I'm looking for something that can find local minima for ...
Cavenfish's user avatar
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6 votes
0 answers
108 views

Is this statement correct: "All structural variations are energy driven"? [closed]

In modelling using molecular mechanics can one state that "all structural variations are energy driven?". The statement is related to protein-ligand binding in modelling. Sometimes one can ...
BND's user avatar
  • 1,341
12 votes
2 answers
286 views

Permissible amount of forces on ions in a relaxed structure

An equilibrium structure would be at a local minimum but that doesn't happen with all relaxation calculations. Relaxed structures tend to have some resultant forces on ions. What amount of these ...
Hitanshu Sachania's user avatar
15 votes
3 answers
200 views

Candidate structures for global minimum determination

What are the best packages that can generate candidate structures for quantum chemical optimization (DFT or CCSD) to find the global minimum? I am working on the gas-phase small inorganic clusters (...
Somnath Bhowmick's user avatar
14 votes
1 answer
413 views

How can I scan the whole PES of a bulk structure?

I am not very familiar with scanning a PES for a bulk structure, and I'd be very appreciative for some suggestions.
Alfred's user avatar
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12 votes
1 answer
243 views

3D Poisson equation solver for arbitrary charge distribution?

I am trying to compute the electrostatic potential profile from a distribution of point-charges that were output from an MD simulation. Does anyone know of ready-made Poisson solver packages that are ...
anneb101's user avatar
  • 995
11 votes
2 answers
187 views

Which SCF energy to use to plot PES after calculations with SMD?

I have a series of molecules calculated (DFT PBE0-D3/def2-TZVP performed in Q-Chem) and I'm ready to plot PES (Potential Energy Surface). I had to increase the grid to get rid of small imaginary ...
Dmitry Eremin's user avatar