Questions tagged [potential-energy-surface]
Questions about potentiology.
13
questions
5
votes
1answer
93 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 ...
5
votes
1answer
108 views
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. ...
9
votes
2answers
108 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 ...
7
votes
1answer
59 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 ...
9
votes
3answers
394 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 ...
10
votes
1answer
139 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.
...
11
votes
2answers
113 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 ...
6
votes
0answers
103 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 ...
12
votes
2answers
157 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 ...
15
votes
3answers
150 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 (...
14
votes
1answer
234 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.
11
votes
1answer
121 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 ...
11
votes
2answers
115 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 ...
