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

Justin Lemkul jalemkul at vt.edu
Wed Jan 2 21:32:49 CET 2013

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


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