[gmx-users] g_dist: extract distances between any two atom pairs

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 3 13:43:37 CEST 2009

Joern Lenz wrote:
> Dear Gromacs Users,
> I need to extract all possible distances between any two atom pairs of a small 
> hexa- to dodecamer from a trajectory. The same is necessary for all dihedral 
> angles of this protein. Now I wonder if this is possible without defining all 
> of them manually in the ndx file and call g_dist for each of them ? Is there 
> a short answer on that ? Maybe I missed the answer to that question in the 
> forum ?!

That level of detail might just require some iterative calls to g_dist and 
g_angle, unfortunately.  Scripts are your friend, here.  Also, g_mdmat might be 
useful, but it plots minimum distances between *residue* pairs, not atom pairs. 
  Much more convenient than repeated calls to g_dist, however :)


> greetings,
> joern
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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