[gmx-users] Interaction across PBC

[Justin Lemkul]

On 4/23/13 6:37 AM, Steven Neumann wrote:
> Dear Gmx users,
>
>
> My protien has got some strong acidic and strong basic parts. I fold and
> unfold my protein with different temperaturss. I bserved high affinity of
> those regions towards each other, they are very close to each other over
> the simulation.
>
> How can I possibly check whether my two regions do not interact across the
> boundary conditions with such high affinity?
>

g_mindist -pi with a suitable index group.

-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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