13
votes
Does increasing Lennard-Jones cutoff means higher accuracy?
I am afraid I can't be of much help regarding the QM part of your simulation, but I can give some thoughts on the MM part. In short: you should use the cutoff that was used to validate your force ...
- 1,948
12
votes
Accepted
Does increasing Lennard-Jones cutoff means higher accuracy?
Very interesting question!
The LJ potential is quite benign in that it has a $r^{-6}$ decay, which is pretty rapid. However, MD codes typically go a bit farther than a straightaway truncation at $r_{\...
- 20k
12
votes
Accepted
Is there any software that is optimized specifically for QM/MM?
pDynamo
pDynamo is a program developed by Martin Field, and is a CHARMM/ORCA interface. There is a wiki.
Here is the first line from the abstract:
The pDynamo program has been developed for the ...
- 1,546
10
votes
What are some of the biggest theoretical and computational challenges in Condensed Phase Chemistry?
The Monte Carlo Sign Problem
For classical systems, Monte Carlo works extremely well. Quantum Monte Carlo is very powerful, but there are many interesting systems that suffer from the sign problem, ...
- 6,794
10
votes
Accepted
How to swap orbitals in ORCA?
I figured out the correct formatting. The section defining the QM needs to have the MORead option, the %moinp section, and the <...
- 1,546
7
votes
Constraining a set of atoms in the MM region using pDynamo (CHARMM/ORCA interface)
To tether a set of atoms (index or fragment) in pDynamo, the below lines are needed (energy model can vary):
...
- 1,546
7
votes
Benchmark transition state geometries in condensed phases
Not really sure about benchmarks for solid state TS geometries. A couple of scattered piece of references are:
(i) This paper by Ceder's group has several related TS barriers: aip.scitation.org/doi/...
- 1,257
6
votes
Accepted
Parameterize a complex that contains Transition metal (Build Force Field)?
I think that the parametrization process is straightforward (but very hardworking!):
select and use an ab initio/DFT software that works well for your metal atoms,
take a look at the force field ...
- 23.9k
6
votes
Is there any software that is optimized specifically for QM/MM?
TeraChem is commercial, but the demo mode will handle calculations taking up to ten minutes and that is free. Ten minutes for a single point energy and gradient gets you pretty far with TeraChem (...
6
votes
Is there any software that is optimized specifically for QM/MM?
TeraChem
QM/MM is not computationally more intensive than regular QM. In mechanical embedding the MM region is essentially free because it's just simple harmonic oscillators. In electrostatic ...
- 8,015
5
votes
Accepted
Defining coordinates using Vector3
In pdynamo 3.0.9
A vector3 can be defined by importing from Geometry module. For example,
...
- 8,015
3
votes
How to model TS for given a small biomolecular system?
So let me summarize your questions: (1) is it possible for a software to automatically draw the electron flow arrows? (2) must the user add and remove the atoms manually, when modelling a TS?
The ...
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3
votes
Recent developments in QM/MM for Molecular Dynamics
Machine Learning
There are several examples about how Machine Learning is been used in Quantum Chemistry. Here I bring two of them that are directly related with QM/MM calculations.
L. Böselt, M. ...
- 23.9k
3
votes
Q-Chem QM/MM options
The Q-Chem manual edition 5.2 is much better at describing QM/MM
However, to answer your main question there are no angles and torsions across a link atom. The link atom is a fictitious hydrogen that ...
- 8,015
3
votes
Accepted
How to localize orbitals in pDynamo (CHARMM/ORCA interface)?
I found the most consistent way to localize orbitals. Use the orca_loc extension. You must create and input file where define the localization method (PM, Boys, ...), and the orbitals you want to ...
- 1,546
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