[gmx-users] Re: Simulation of 2D lattice model

Justin Lemkul jalemkul at vt.edu
Wed Jan 2 16:11:13 CET 2013

On 1/2/13 9:26 AM, James Starlight wrote:
> by the way also I'd like to know what options for the pbc should I
> specify that my system looked like infinite lattice in the x-y dims ?

Do you want the lattice to be infinite or do you just want it to look like it's 
infinite?  If you want an infinite lattice, you need to build it such that bonds 
can be formed across periodic boundaries, in conjunction with the .mdp keyword 
periodic_molecules set to "yes."  This is the approach many people take when 
simulating graphene sheets or CNT.  See the list archive for extensive discussions.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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