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Author: Subject: How to apply constant force on a molecular structure?
jimmyeeh
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[*] posted on 6-3-2015 at 07:27
How to apply constant force on a molecular structure?


Guys, I'm using HyperChem 8 and I have a graphene. The thing that I want to do is to simulate the application of a force only on one molecule of that graphene, and I want the force to constantly push.

In order to do that I see that I can set an initial velocity for the specified atoms, but it fades away (naturally).

Is there a way to set the molecule to be "pushed" at a constant force?

And a bonus question :) :

If I'm "kicking" the graphene in the early-mentioned spot (the benzen molecule), can I keep the border atoms fixed (the graphene border atoms)? In order to observe the wave that will be formed from the constant force?

It would really help me out and I could be owing you (in a few years) a career in science :D.

Best regards,
Razvan

[Edited on 6-3-2015 by jimmyeeh]

[Edited on 6-3-2015 by jimmyeeh]
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Polverone
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[*] posted on 6-3-2015 at 11:35


I don't know about Hyperchem specifically but it sounds like you are doing a molecular mechanics/molecular dynamics calculation or series of calculations. In most MM packages there are options to freeze the coordinates of certain atoms. So if you have a graphene sheet it sounds like you would want to freeze a few atomic coordinates near the center, and also freeze atomic coordinates for atoms around the edge of the sheet. To see the sheet deform as the center is "pushed in," you would change the central atom frozen coordinates in succession and perform a corresponding series of MM or MD calculations.

That said, I am not sure what you are trying to model and whether this approach makes sense. MM models usually do not handle bond breaking or formation. You will get enormous unphysical strains that may cause complete numerical breakdown if you try to "push" your central atoms too far.




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jimmyeeh
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[*] posted on 8-3-2015 at 01:36


Yep, this is what I'm trying to do. To keep the edge of the sheet frozen and make something like a drumming effect somewhere inside the sheet (to apply that force repeatedly) and see how the sheet makes waves.

Can you recommend me a specific program?

I will also try your advice with the changing coordinates for that specific spot, though I thought I could make it automatic. Thank you very much.
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[*] posted on 8-3-2015 at 12:15


You're not going get to a "drumming" effect from what I've proposed. Each calculation starts from a new geometry with no history. If you run a molecular dynamics simulation at finite temperature you will see persistent thermal motion in the non-frozen atoms. Otherwise the system, if numerically stable, will find the nearest local minimum and stay there.

What is your driving motivation for doing this sort of calculation? It is not physically grounded. If you want to study behaviors of nanodevices or something you should explain a little more about what you're trying to model.

There are several fine free molecular mechanics/dynamics packages. GROMACS and NAMD would probably be good choices if you are simulating with classical physics only (no bond breaking/formation, no quantum effects of any sort). I don't know if there are any easy-to-use graphical user interfaces for them. When I used them ~10 years ago everything was set up from scripts and command line arguments. In most packages you will probably have to resort to scripts to set up calculations like I described in my first response to you, because it is not a typical workflow that someone else is likely to have developed a user interface for.




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jimmyeeh
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[*] posted on 14-3-2015 at 06:13


Yep, I understand what you are saying. I don't know for sure what my teacher has instored for me, but this is what he asked. I managed to find the HyperChem option of fixing atoms (apparently it was a v8.0 built-in thing) and now I'm trying to figure out how to give velocities to the chosen interior atoms at some time interval, because I don't want them to stop after running the Molecular Dynamics option.

When I find out more, I'll keep you updated.
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[*] posted on 9-5-2015 at 05:38


I'm not sure what exactly you are asking for. It sounds like you are trying to do a geometry optimization under deformed conditions or something through-out time.

By only one molecule do you mean one monomer?

I don't know exactly how this could be done using the soft-ware you're talking about but if you're going the DFT route this sounds seriously involved and might require two pieces of soft-ware and a lengthy computation time.




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