[gmx-users] g_dist: extract distances between any two atom pairs
erikm at xray.bmc.uu.se
Wed Jun 3 22:23:00 CEST 2009
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 :)
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Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
erikm at xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
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