[gmx-users] periodic boundary condition

[David van der Spoel]

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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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