Dear all,
I am planing to do pulling on a bundle of elongated proteins. I compared
two box types - triclinic and
dodecahedron. The volume and total number of atoms (protein+solvent),
following the editconf and genbox commands,
were 522.06 nm3 and 47921 for triclinic box and 2444.19 nm3 and 242222 for
dodecahedron.
Although dodecahedron box has always been suggested due to shortcomings in
the periodic interactions for a triclinic box, but
I have seen examples of the use of triclinic box. Due to this huge
difference in the number of solvents in the two cases
I am tempted to use triclinic box, but I am a bit confused. Any ideas or
suggestions?
regards,
cyrus
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