Questions tagged [potential-energy-surface]

Questions about potentiology.

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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 ...
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1 answer
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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 ...
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  • 161
6 votes
2 answers
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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 ...
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8 votes
1 answer
157 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 ...
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9 votes
2 answers
265 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 ...
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5 votes
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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 ...
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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. ...
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9 votes
2 answers
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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 ...
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8 votes
1 answer
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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 ...
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  • 498
9 votes
3 answers
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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 ...
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1 answer
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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. ...
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11 votes
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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 ...
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6 votes
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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 ...
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12 votes
2 answers
160 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 ...
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15 votes
3 answers
157 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 (...
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14 votes
1 answer
250 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.
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12 votes
1 answer
154 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 ...
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11 votes
2 answers
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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 ...
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