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

[Justin Lemkul]

On 8/27/18 9:37 AM, Javier Luque Di Salvo wrote:
> 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.

gmx distance -oall with two selections (all atoms A and all atoms B) 
should give you what you want, or if you're only interested in a given 
polymer's atom A and all other B, you can select those groups, as well.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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