Molecular dynamics simulation - Revision history

Apm: added link to yet unwritten page Molecular dynamics implementation cheat sheet

2022-04-30T09:00:41Z

added link to yet unwritten page Molecular dynamics implementation cheat sheet

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	~~{{Stub}}~~

	This is about non-quantum-mechanical classical mass and spring simulations of molecular systems. <br>		This is about non-quantum-mechanical classical mass and spring simulations of molecular systems. <br>
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	== Related ==		== Related ==

			* '''[[Molecular dynamics implementation cheat sheet]]'''
	* [[Design of Crystolecules]]		* [[Design of Crystolecules]]
	* [[NanoEngineer-1]]		* [[NanoEngineer-1]]

Apm: /* Suitability for simulation of cog & gear style gemstone based nanomachinery */ added link to page Limits of construction kit analogy and more

2022-04-29T15:37:42Z

Suitability for simulation of cog & gear style gemstone based nanomachinery: added link to page Limits of construction kit analogy and more

← Older revision		Revision as of 17:37, 29 April 2022
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	* Electron deficiency atoms like e.g. [[boron]] and [[aluminum]]		* Electron deficiency atoms like e.g. [[boron]] and [[aluminum]]
	* Metal atoms – electron gas – electron deficiency bonds – ...		* Metal atoms – electron gas – electron deficiency bonds – ...
	* Weakly bonded ~~third row and higher~~ halogenides [[iodine]] and [[~~bromine~~]]		* Weakly bonded halogenides (e.g. [[iodine]], [[bromine]]) under load and contacting electron donors - this asks for a reaction
			* See related topic: "[[Limits of construction kit analogy]]" and "[[Construction kit analogy for the periodic table of elements]]"

	Regarding the accuracy of predictions for the level friction losses from such simulations the situation is less clear cut. <br>		Regarding the accuracy of predictions for the level of friction losses from such simulations the situation is less clear cut. <br>
	See related paper: [[Evaluating the Friction of Rotary Joints in Molecular Machines (paper)]] and [[Friction in gem-gum technology]] <br>		See related paper: [[Evaluating the Friction of Rotary Joints in Molecular Machines (paper)]] and [[Friction in gem-gum technology]] <br>
	Overall the predictions for friction are very favorable for feasibility of practically useful highly performant production and other devices.		Overall '''the predictions for friction are very favorable for feasibility of practically useful highly performant production and other devices'''.

	== The three kind of springs ==		== The three kind of springs ==

Apm: added section == Suitability for simulation of cog & gear style gemstone based nanomachinery ==

2022-04-29T15:29:38Z

added section == Suitability for simulation of cog & gear style gemstone based nanomachinery ==

← Older revision		Revision as of 17:29, 29 April 2022
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	For things like [[tooltip chemistry]] in [[piezomechanosynthesis]] more accurate [[quantumchemistry simulation]] metods are needed.		For things like [[tooltip chemistry]] in [[piezomechanosynthesis]] more accurate [[quantumchemistry simulation]] metods are needed.

			== Suitability for simulation of cog & gear style gemstone based nanomachinery ==

			Unlike in the problem of predicting the folding of natural proteins (a common application of molecular dynamics) <br>
			nanomachinery out of [[crystolecule]]s will typically be designed to not feature highly unstabel states where <br>
			tiny differences in the starting conditions leads to vastly different states at the end of the simulation (the hallmark of chaotic systems).

			Concrete example:
			* A half folded protein might be at a state where a tiny nudge leads to completely different folding states. E.g. one ball-like, one rod-like.
			* A diamond bearing in operation needs an extremely brutal "nudge" that obliterates it (deshells it) to end up in a state vastly apart from prediction.

			In short: [[Gem-gum]] nanomachinery is robust against perturbations. <br>
			As such '''successful nanomachinery operation in simulations indicates real-world functionality with very high reliability'''. <br>
			Well, that is as long as material strains are not put to the absolute limit (easy) and other potential issues are engineered around.<br>
			Potential issues include badly modeled:
			* B-N [[coordinative bonds]]
			* Electron deficiency atoms like e.g. [[boron]] and [[aluminum]]
			* Metal atoms – electron gas – electron deficiency bonds – ...
			* Weakly bonded third row and higher halogenides [[iodine]] and [[bromine]]

			Regarding the accuracy of predictions for the level friction losses from such simulations the situation is less clear cut. <br>
			See related paper: [[Evaluating the Friction of Rotary Joints in Molecular Machines (paper)]] and [[Friction in gem-gum technology]] <br>
			Overall the predictions for friction are very favorable for feasibility of practically useful highly performant production and other devices.

	== The three kind of springs ==		== The three kind of springs ==

Apm: /* Computational complexity */ added linebreaks

2022-04-29T14:43:28Z

Computational complexity: added linebreaks

← Older revision		Revision as of 16:43, 29 April 2022
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	quickly become quite computationally expensive and slow.		quickly become quite computationally expensive and slow.

	Calculating all non-local interactions of atoms gives (n^2-n)/2 interactions to handle.		Calculating all non-local interactions of atoms gives (n^2-n)/2 interactions to handle. <br>
	So this would scale with O(n^2). Practically a cutoff distance is implemented.		So this would scale with O(n^2). Practically a cutoff distance is implemented. <br>
	Unfortunately such a cutoff is not sufficient to drop the complexity down to O(n).		Unfortunately such a cutoff is not sufficient to drop the complexity down to O(n).

	The problem are indirect interactions of the kind:		The problem are indirect interactions of the kind: <br>
	Atom1 pushes atom2 pushes atom three pushes .... pushes atom N.		Atom1 pushes atom2 pushes atom three pushes .... pushes atom N. <br>
	Where in naive molecular dynamic simulation implementations it will take		Where in naive molecular dynamic simulation implementations it will take <br>
	n steps for the pushing to propagate n atoms.		n steps for the pushing to propagate n atoms. <br>
	Worse if the equilibration is a wave needing to run back and forth the chain of atoms several times to reach a state near equilibrium.		Worse if the equilibration is a wave needing to run back and forth the chain of atoms several times to reach a state near equilibrium.

Apm: added link to new page quantumchemistry simulation and related pages to the intro.

2022-04-29T14:42:38Z

added link to new page quantumchemistry simulation and related pages to the intro.

← Older revision		Revision as of 16:42, 29 April 2022
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	Especially in the case of [[crystolecule]]s their dynamic behavior is usually not at all sensitive on small <br>		Especially in the case of [[crystolecule]]s their dynamic behavior is usually not at all sensitive on small <br>
	inaccuracies/perturbations which can be the case for protein folding problems.		inaccuracies/perturbations which can be the case for protein folding problems.

			For things like [[tooltip chemistry]] in [[piezomechanosynthesis]] more accurate [[quantumchemistry simulation]] metods are needed.

	== The three kind of springs ==		== The three kind of springs ==

Apm at 22:16, 21 November 2021

2021-11-21T22:16:10Z

← Older revision		Revision as of 00:16, 22 November 2021
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	* [https://en.wikipedia.org/wiki/Computational_complexity Computational complexity]		* [https://en.wikipedia.org/wiki/Computational_complexity Computational complexity]
	* [https://en.wikipedia.org/wiki/Hooke%27s_law#Matrix_representation_.28stiffness_tensor.29 Stiffness Tensor]		* [https://en.wikipedia.org/wiki/Hooke%27s_law#Matrix_representation_.28stiffness_tensor.29 Stiffness Tensor]

			[[Category:Pages with algorithms]]

Apm: /* Related */ added link to page Design of Crystolecules

2021-11-21T11:19:09Z

Related: added link to page Design of Crystolecules

← Older revision		Revision as of 13:19, 21 November 2021
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	== Related ==		== Related ==

			* [[Design of Crystolecules]]
	* [[NanoEngineer-1]]		* [[NanoEngineer-1]]
	* {{todo\|add notes on existing models}}		* {{todo\|add notes on existing models}}

Apm: /* The three kind of springs */

2021-11-21T11:18:11Z

The three kind of springs

← Older revision		Revision as of 13:18, 21 November 2021
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	* bond bending relative to other bonds		* bond bending relative to other bonds
	* bond torsion over three bonds - dihedral angle		* bond torsion over three bonds - dihedral angle

			'''MD simulation models need two things:'''
			* The force field models – how forces/moments change with lenght-changes and angle-changes
			* Parameters for these models

	== Computational complexity ==		== Computational complexity ==

Apm at 11:16, 21 November 2021

2021-11-21T11:16:21Z

← Older revision		Revision as of 13:16, 21 November 2021
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	* [[NanoEngineer-1]]		* [[NanoEngineer-1]]
			* {{todo\|add notes on existing models}}

	== External links ==		== External links ==

Apm at 11:15, 21 November 2021

2021-11-21T11:15:16Z

← Older revision		Revision as of 13:15, 21 November 2021
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	inaccuracies/perturbations which can be the case for protein folding problems.		inaccuracies/perturbations which can be the case for protein folding problems.

			== The three kind of springs ==

			There are three forces/moments that nead to be treated: <br>
			stretchning/compression, bending, and torsion

	* bond stretch and compression - e.g. modeled by the Lennard Jones potential		* bond stretch and compression - e.g. modeled by the Lennard Jones potential