[gmx-users] Peptide distance matrix

[Justin Lemkul]

On 4/15/13 12:08 PM, Steven Neumann wrote:
> And last question:
>
> Are these minimum distances averaged over the simulation time? Cannot find
> any equation the way it is calculated... in Manual its written:
>
> This minimum distance between two residues Ai and Aj is defined as the
> smallest distance between any pair of atoms (i 2 Ai, j 2 Aj ). The output
> is a symmetrical matrix of smallest distances between all residues.
>
> And nothing else...
>

The question is answered by reading g_mdmat -h.

-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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