Build crystal

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Build crystal

kaio
Hello,
I would like to have some help regarding crystal building because I can't make it work. Does someone already used this functionnality ?
 Thanks.
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Re: Build crystal

agilemolecule
Administrator
kaio wrote
Hello,
I would like to have some help regarding crystal building because I can't make it work. Does someone already used this functionnality ?
 Thanks.
What is the concrete problem?











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Re: Build crystal

mfennim
In reply to this post by kaio
Perhaps I can help. After selecting the build crystal function, choose what type of crystal you want to make in the "crystal system" box (cubic, tetragonal etc). Select the number of replicas you want to include in your crystal by adjusting the "Cell Copies" tab. In my experience, you should chose you Cell Parameters (i.e. the distance between your copied particles) such that there is minimal or no overlap. Overlapping molecules can be problematic because of the huge intermolecular forces generated, which will blowup your model upon running MD or MC. Either way, you should perform a short minimization by clicking the "Remove Clashes" button. Then, I would setup PBC at very low density and themalize your model by increasing the pressure via Borostat (I usually start out at 2500atm) at initially low temperature using the Berendsen Thermostat. When your crystal starts to approach your desired density, stop the simulation, and save the model. Restart the simulation, at a lower pressure (e.g. 100-200atm) and thermalize your crystal at the desired temperature (again using Berendsen scheme). I usually thermalize for at least 50ps. At the end of the thermalization, check that the average density is at the correct value. If it is, great. You're done. If not, adjust the borostat up or down, and re-thermalize. \

Hope this helps
Mark
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Re: Build crystal

agilemolecule
Administrator
Thanks for the help Mark.

Unfortunately, I can not give a full description. Are described only those things that in my view are difficult. However, it is difficult to see from inside what is simple, and what is not. Could you write what things cause you to have difficulty when getting acquainted with the program?




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Re: Build crystal

mfennim
Have you given any thought in creating a tab, where users can post examples and descriptions of their work? I've run simulations with great accuracy with Abalone and Ascalaph (and now attempting with MDynamix) and would be willing to post for the benefit of new users.

Mark
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Re: Build crystal

agilemolecule
Administrator
mfennim wrote
Have you given any thought in creating a tab, where users can post examples and descriptions of their work? I've run simulations with great accuracy with Abalone and Ascalaph (and now attempting with MDynamix) and would be willing to post for the benefit of new users.

Mark
There are Wiki-like pages:
http://www.layruoru.com/dokuwiki/doku.php/molecular_mechanics_-_it_is_simple