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

[silvester.thu]

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?

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.

Thanks.






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Shao Yue
Institue of Biomechanics and Biomedical Engineering
Department of Engineering Mechanics
Tsinghua University
P.R. China
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