[gmx-users] Linear CG beads, grompp doesn't work

[Justin Lemkul]

On 1/1/13 10:46 PM, Xu Dong Huang wrote:
> Dear Justin,
>
> My .itp does not contain angles or dihedrals because we are simply interested in the very simple generic case of a linear (what we assume by defining a coordinate file of linear beads) polymer model. I will go through the tutorial and try to see if it resolves my issue.
>

The molecule will not remain linear simply due to consecutive bonds.  Hopefully 
the tutorial explains some of the necessary methodology for creating species 
that are indeed to be kept linear, though the example therein (CO2) is 
considerably less complex than what you seek to do.

-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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