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Mistakes when building crystal
#16589 01/05/08 01:52 AM
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Hi Charmmers:
When I build the following crystal:
******
Crystal Define hexagonal 14.00147 14.00147 10.33808 90.00000 90.00000 120.00000

! build the crystal along with the images within the cutoff
crystal build cutoff 20 Noper 5
( X -Y, X ,1/6 +Z)
(-Y , X -Y,1/3 +Z)
(-X , -Y ,1/2 +Z)
(-X +Y, -X ,2/3 +Z)
( Y , -X +Y,5/6 +Z)
******
It ended up with:
IMFILL> WARNING: Transformation 118 has no inverse. Check Crystal Operations.
******
As a beginner, I am wondering whether it is a mistake related with the transformation operations, I should check back my specific coordinate input? Thanks

Re: Mistakes when building crystal
Hailiang #16590 01/05/08 03:09 AM
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It is the transformations; several appear to have both X and Y in one of the comma separated terms, which is not consistent with the P21 example in crystl.doc

Re: Mistakes when building crystal
rmv #16591 01/05/08 03:22 AM
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Thanks a lot for your reply, but since those transformations involve rotations increasing by 60deg, I think thats why both X and Y appears. Maybe there is still something which I dont realize causing the "no inverse" problems?

Re: Mistakes when building crystal
Hailiang #16592 01/05/08 05:06 PM
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There are rotations for P21 as well. What is the source of the transformations you are trying to use?

Every image transformation must be reversible, i.e. it must have an inverse.

Re: Mistakes when building crystal
rmv #16593 01/07/08 01:22 AM
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Thanks a lot rmv. I posted my new story in the next.

Re: Mistakes when building crystal
Hailiang #37894 05/26/20 11:44 AM
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Hello, I know it is a question very long time ago, but I wonder how was it resolved. I encountered the same exact problem using same exact symmetry transformation. The crystal has P61 space group. And I got its symmetry transformations from http://img.chem.ucl.ac.uk/sgp/large/169az1.htm Did I do something wrong or is there something wrong in crystal.src? CHarmm version is c42b2.

Last edited by Allen_123; 05/26/20 11:54 AM.
Re: Mistakes when building crystal
Hailiang #37895 05/26/20 06:14 PM
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I'm not sure if there's a bug or not myself; the code is over 30 years old, and the original author has not been actively involved in CHARMM development for quite some time. It is possible there's an expression parsing issue, I suppose.

Do you intend to run a simulation on an asymmetric unit, or do you just want to use the crystal transforms for model building to build the complete unit cell?


Rick Venable
computational chemist

Re: Mistakes when building crystal
rmv #37896 05/27/20 01:26 AM
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Thank you. I intend to build the complete unit cell or maybe several unit cells. In this case, I will try to build the unit cell myself.

Re: Mistakes when building crystal
Hailiang #37899 05/28/20 08:57 AM
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I think there might be another bug in translation of unit cell(Noper=0) for hexagonal type crystal. I got pdb of unit cell of same P61 crystal from CCDC and implemented into Charmm, and run a short NPT simulation after minimization. There was no error, but the IMNBvdw term was extremely large (28826012849). I wrote the image atoms and found an overlap of two unit cells([img]https://imgur.com/e9shgpM[/img]) The correct packing should look like this [img]https://imgur.com/iBjOTbB[/img]

Last edited by Allen_123; 05/28/20 09:11 AM.
Re: Mistakes when building crystal
Hailiang #37900 05/28/20 05:46 PM
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There can be different choices for the orientation of the hexagon in the xy plane, and there can also be a difference between symmetric and aligned coordinate conventions.


Rick Venable
computational chemist


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