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

James Starlight jmsstarlight at gmail.com
Wed Jan 2 21:08:08 CET 2013


I want to simulate flexible lattice consist of only one type of atoms
(nodes). So the planar (sp2 ) carbons are rigid. On other hand more
flexible (sp3) carbons  connected with hydrogens but I want that
hydrogens were not included in my lattice. Should I use another
(what? )atom-type for the node of my lattice ?


2013/1/2, Justin Lemkul <jalemkul at vt.edu>:

> The valence of an atom is whatever you assign it in the topology.  Carbon
> atoms
> can be planar, as in aromatic rings of amino acids, without any issue.
> -Justin

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