Author Topic: molecular dynamic and optimize Geometry  (Read 67 times)

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Offline mohit.s

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molecular dynamic and optimize Geometry
« on: February 7, 2018, 05:36 »
Hi
A. What are the differences between molecular dynamic simulation and optimize Geometry?
B. Which one is more suitable to determine the relative coordinates of the nanotubes and molecules on their surface (for energy  and forces calculations )?

Offline Ulrik G. Vej-Hansen

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Re: molecular dynamic and optimize Geometry
« Reply #1 on: February 7, 2018, 08:38 »
A: MD is, as the name implies, a way of simulating the dynamics of a system under certain conditions. Optimize geometry is a way to find the minimum energy structure, which is often the one dominating the properties of the system - at least to a good approximation.

B: That essentially depends on whether you want to model zero-temperature or finite temperature, and what kind of analysis you would like to make.

Offline Petr Khomyakov

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Re: molecular dynamic and optimize Geometry
« Reply #2 on: February 7, 2018, 10:29 »
To add to the previous post, you may take a look at https://en.wikipedia.org/wiki/Molecular_dynamics and https://en.wikipedia.org/wiki/Energy_minimization and references therein. But if you really want to understand all these things, you may consider reading some textbooks and original articles related to your system of interest; search for it in Google Scholar or Web of Science.

Offline mohit.s

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Re: molecular dynamic and optimize Geometry
« Reply #3 on: February 11, 2018, 05:15 »
Thank you for your reply,
In an article I read: "The coordinates cannot be calculated simply by system relaxation from density functional theory  (DFT) simulations because DFT cannot estimate van der Waals forces correctly, and these play an important role in the interaction between the nanotube and the amino acid".
 is it correct?

Offline Petr Khomyakov

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Re: molecular dynamic and optimize Geometry
« Reply #4 on: February 12, 2018, 09:50 »
If we are talking about DFT as an exact theory, it is able to account for dispersion interaction. But approximate density functionals (LDA and GGA) implemented  in QuantumATK do not account for these interactions, and one should try using DFT-D correction schemes as discussed at  https://docs.quantumwise.com/tutorials/dispersion_corrections_and_bsse/dispersion_corrections_and_bsse.html.