Cherry Y. Yates wrote:
Dear gromacs developers and users,
I am calculating a nanotube which has periodic boundary condition along
one direction. I wonder how to make an itp file for this system. The
difficulty lies in describing the bond between two end atoms, e.g., two
atoms are bonded in an infinite length system, but are located on the
bottom and top of a unit cell.
use x2top
and in your mdp file use pbc=full
Thanks,
Cherry
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
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