[gmx-users] Calculate and print ALL distances between atoms A and B from structure file (i.e. not over time), with detailed information

Javier Luque Di Salvo jluquedisalvo at gmail.com
Mon Aug 27 17:37:44 CEST 2018

Dear users,

I am trying to calculate ALL distances between two types of atoms, say atom
A and atom B. The system is a polymer composed of 20 linear chains. Each
chain has 1 (one) atom A that can form a crosslink with some atom B of an
adjacent, near chain. Thus, in order to generate such crosslinks
(self-crosslinks are not necessarily excluded), I run NVT and NPT
simulations to compress the linear chains and bringing them together. At
some point, when the chains are closer, I need to analyze distances A-B
that fall within a certain cutoff, in order to decide if a bond can be
formed and added following the specbonds.dat topology directives.

I tried with mindist, distance, pairdist, but I was not able to generate an
output that specifies all the distances among a given atom A and all atoms
B. This output should contain either the atom number/ chain/ residue of
each atom involved in the distance calculation. Atom type B is present on
each linear chain 15 times; if no cutoff is specified, the output should
contain (15x20) distances for each A atom; i.e. 15x20x20 distances.

Currently I can identify only the minimum distance between atom A and B,
but I am a bit lost in how to generate the more detailed output as
described above. Any guidance is appreciated.

Best regards


*Javier Luque Di Salvo*

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