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

[Justin Lemkul]

On 1/2/13 3:08 PM, James Starlight wrote:
> Justin,
>
> 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 ?
>

I'm sorry to say I don't understand what you're saying.  If you want a lattice 
of carbon atoms, you can surely develop a united-atom model of such a lattice 
and never involve hydrogen atoms of any sort.  Again, valence depends entirely 
upon what you define in the topology or its precursors (.n2t or .rtp).

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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