> I want to build a supercell of 2*2*1 from the .cif
> file. I am using super cell option in avogadro. When I open my .cif file, I
> see some broken molecules (not complete structures). As this broken
> molecules create trouble in generating input for MD runs.
My guess is that you have molecules spanning cell boundaries. There aren't many
good options for how to handle this. My personal suggestion would be to select
and remove these fragments.
But to give more advice, I'd need to know what your CIF is.
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
twitter: @ghutchis
web: https://hutchison.chem.pitt.edu/
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