[gmx-users] Clarification on gmx mindist

Sampurna Mukherjee sampurnamukherjeebiology at gmail.com
Thu May 17 10:06:04 CEST 2018

             This is in context of protein-protein simulation.One of my
protein is a 167 residue chain(receptor), the other protein is a 41 residue
peptide (ligand).
                                 I am using mindist with the -or option to
see how my ligand comes close to my receptor protein.

I have the following questions:
1) When we say minimum distances ( my index file has atoms of ligand saved
as ligand and receptor atoms saved as receptor, I am calculating mindist
between these two groups), what exactly is being calculated? Does it mean
the minimum distance from any atom of ligand to any atom of the receptor?
2)Can anybody clarify more on the phrase " minimum distances to each
residue in the first group are determined and plotted as a function of
residue number." ?
3) Minimum distance is being calculated between which quantity? (e.g
C-alpha or Centre of Mass ?)

and finally , is my approach correct for my system?


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