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 :)
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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