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

Erik Marklund 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 :)
> -Justin
>> greetings,
>> joern
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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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