[gmx-users] how to build the input files of an infinite system

[Mark Abraham]

silvester.thu wrote:
> Hello everyone,
>  
> I am working on a simulation of an infinite system but I do not know how 
> to build its periodic boundary conditions in GROMACS. My system is a 
> graphene that is infinite on a certain direction. Surely I can not 
> generate an infinitely large graphene for input. So I want to make a 
> finite graphene to repeat along a certain direction in order to 
> approximate the "infinite" one (e.g: spread the finite graphene from 
> left to right). But I do not know the technical details. Anyone have 
> experience on this kind of problems?

Yes. You can probably adapt the advice here
http://wiki.gromacs.org/index.php/Carbon_Nanotube to your needs.

> I have tried to use the PBC in GROMACS, and add the bonds, angles and 
> dihedrals between atoms on the left edge and atoms on the right edge and 
> make the size of box to be just the same as the sum of length of C-C 
> bond and the width(the distance from the left edge to the right edge) of 
> graphene. But it did not work.
>  
> Anyone can give me some advice? It will be very helpful.

Describing failure with "It did not work" makes it impossible for us to
give free advice at a rate that is worth our time. A detailed
description of what you did and what happened is almost always much more
valuable and a better use of everybody's time than the alternative :-)
See the advice here http://wiki.gromacs.org/index.php/Support

Mark