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Hello Charmm users,

I am trying to simulate a hexagonal molecular crystal and hope to start from a unit cell. According to Charmm manual, hexagonal unit cell has a volume of V=sqrt(0.75)*a^2*c. The only possible choice is a prism with a base of parallelogram that has angle of 60-120. Therefore, if I use ' crystal build HEXA a a c 90 90 120 and crystal build noper 0 cutoff ', image operation will be purely translational like the second image in attachment. [img]https://imgur.com/HoSOoPL[/img] However, this will not be the correct way to pack a hexagonal prism.(first pic of attactment). [img]https://imgur.com/HoSOoPL[/img] My question is that 'what is the unit cell of hexagonal crystal? and what is the proper symmetry operation? If the unit cell strut is like what I think, how should I alter the symmetry operations(probally not use Nope 0) in order to fully mimic a hexgonal prism.

Last edited by Allen_123; 04/20/20 09:07 AM.
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rmv Online Content
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You may be confusing the lattice type (unit cell) with the molecular symmetry; the latter represents the operations needed to generate the symmetry related copies of an asymmetric unit.


Rick Venable
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Well, if initial structure is a unit cell instead of an asymmestric unit, I still need symmetry copies that repeat the unit cell(in this case,translation only (P1)).
And that's why I need the command 'crystal build noper 0 cutoff ...' But, I'm confused about the shape of unit cell of hexagonal lattice type. Is it a parallelogram based prism or simply a hexagonal prism since both of them could have edge 'a, a, c and angle 90 90 120' . If it is the former, then I need more symmetry operations other than translational (see the first image in the link of post). The P1 translation results in incorrect packing of unitcell. If the unit cell is a hexagonal prism, then there must be a mistake in Charmm's documation since the volume of it should be 3*sqrt(0.75)*a^2*c instead of sqrt(0.75)*a^2*c. I don't know which case is true.

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I just found a previous post mentioning that there is a mistake in charmm's manual that hexagonal cell should have a volume of 3*sqrt(0.75)*a^2*c instead of sqrt(0.75)*a^2*c, indicating that the unit cell is indeed a hexagonal prism. I'm confirming that it is correct. Thank you!
https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=15115

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The cell is a hexagon in the xy plane, i.e. when viewed along the z axis.


Rick Venable
computational chemist


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