Justin A. Lemkul skrev:
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 ?!
Actually, this is one reason why open source is such a fantastic thing!
With a little C-skill that functionality ought to be relatively simple
to incorporate in some existing analysis tool. Not saying that it takes
less time than scripting multiple calls to g_dist, but it can be reused
in the future.
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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-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
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