23 votes

In molecular mechanics, how are van der Waals forces modelled?

Additional to Alone Programmer's answer. The Lennard-Jones Potential (LJ 12-6) is the standard, but is not unique, in some cases the factor of 6 is changed to 8 to simulate better the hydrogen bonds. ...
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In molecular mechanics, how are van der Waals forces modelled?

First I will try to directly answer this question: In terms of energy, how are van der Waals forces modelled (are there formulas that govern these)? The most common way to model the potential ...
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20 votes

In molecular mechanics, how are van der Waals forces modelled?

You are looking for Lennard-Jones potential. Basically, the interatomic interaction is modeled by this formula: $$U(r) = 4 \epsilon \Bigg [ \Big ( \frac{\sigma}{r} \Big )^{12} - \Big ( \frac{\sigma}{...
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What is the cutting edge for open-source Force-Field generation?

ForceBalance ForceBalance is one approach which aims at making it easier to create force fields from a combination of theoretical and experimental data. I believe it's within the OpenMM framework. The ...
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Why can MD simulations not handle "exotic" materials?

"But they cannot handle "exotic" materials. Why?" You have claimed this without a reference! MD in principle can be done for any group of interacting particles, especially if you ...
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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 ...
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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_{\...
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10 votes

What is the cutting edge for open-source Force-Field generation?

ForceBalance Cody is right, ForceBalance is designed for the task of generating custom force fields. Force fields have a lot of variability in their functional forms, representation of parameters (as ...
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8 votes

Why can MD simulations not handle "exotic" materials?

By molecular dynamics, I assume you mean molecular dynamics using force-fields (a.k.a. Classical Molecular Dynamics). Remember that there is also ab initio MD. Force fields are parameterised, i.e. ...
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7 votes

Symmetry-preserving low-level structural relaxation

ASE has a FixSymmetry constraint that preserves spacegroup symmetries. It works with a variety of structure optimization algorithms. You could use LAMMPS as the engine or one of the many other ...
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Rule-of-thumb for Morse potential cutoff in molecular dynamics?

Since you are referring to "the Morse potential", I assume you mean to use it for modeling van der Waals interactions? If not, please ignore this answer and consider updating your question to include ...
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7 votes

How to calculate the nuclear energy derivatives in molecular mechanics?

You iterate through the bond, angle, torsion, etc. contributions and sum the gradients on each atom. When we were implementing these for Open Babel, we found a very nice dissertation which gave some ...
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6 votes

How to calculate the nuclear energy derivatives in molecular mechanics?

Typically, force evaluation happens in Cartesian coordinates regardless of the approach (QM or MM). In QM codes the forces may then be projected into internal coordinates, which in turn is usually ...
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6 votes
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Empirically determining thermostat damping factor

To the best of my knowledge, there is no universal or even near-universal heuristic for what the time constant should be. The only rule of thumb I have encountered is that the time constant should be ...
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Symmetry-preserving low-level structural relaxation

GULP GULP (General Utility Lattice Program) uses specific forcefields for different type of systems and it is designed to work with periodic conditions. Also, it has defined several type of potential ...
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The number of long-range interaction pairs in Tinker

The charge-charge interactions are only including things which aren't "bonded", this includes angles, and sometimes 1,4 Torsions. This is because the electrostatic interaction is already ...
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