So I've removed pbc from the structure and defined new box dims by
editconf. Now how I could cut all atoms which are not inclluded to
that box ( water in upper and lower leaflets) ? As I told when I did
it by means of genbox -cs b2ar_Smaller.gro -box 8.68740 8.41864
9.70145 atom order of the protei
Hi Tsjerk!
1-Could the hexagonal prism be used with the membrane contained system
? Could you show me visual example of such pbc for bilayer-like
systems ?
2-Have GROMACS build-in utilities for such deletion of the atoms
within specified cut-offs ( e.g above or below specified distanses)
James
Hi James,
It's probably better to put all the molecules in the original box (trjconv
-pbc mol), and then delete all molecules with an atom with z<0 or z>9.7. In
addition, why not use a hexagonal prism to limit the size of your system
further? Saves and additional 14%.
Hope it helps,
Tsjerk
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