[gmx-users] Peptide distance matrix

Justin Lemkul jalemkul at vt.edu
Mon Apr 15 18:19:07 CEST 2013

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


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