[gmx-users] Parsing g_rms binary rmsd comparison matrix

Mark Abraham mark.j.abraham at gmail.com
Wed Mar 5 13:23:11 CET 2014

On Mar 4, 2014 9:19 PM, "João Henriques" <joao.henriques.32353 at gmail.com>
> Hello everyone,
> Let me start by saying that I am unsure whether this is a question for the
> gmx-users or gmx-developers mailing list, but here it goes:
> I have written a Python/NumPy script that parses the rmsd comparison
> dumped by g_rms in the .xpm format. However the "nlevels" are not
> sufficient to give me the desired detail for posterior calculations.
> Therefore I have decided to forget the .xpm and focus on the binary dump
> produced by g_rms using the flag -bin. My sole purpose is to fetch the
> binary rmsd data and pass it into an array, so that I can then do some
> calculations over it.
> I am a total newbie in binary file parsing, but I know that I can, for
> example, use something like "numpy.fromfile" for that purpose. The problem
> is that I have absolutely no idea of what is the structure of the binary
> rmsd comparison matrix file. I'm pretty sure that besides the actual data,
> there are other stamps and stuff being written to the file, with
> potentially different formats as well. I tried looking at gmx_rms.c but I
> got lost very quickly.

No, g_rms -bin is very plain, see

Do let us know how you go!


> Is there anyone out there that might be able to help me identify the
> correct structure OR is there any Python or C++ routine capable of doing
> similar things to what I need? I have no urge in "reinventing the wheel".
> P.S.: I know that there is the possibility of modifying g_rms itself, but
> that is not what I'm looking for.
> Thank you in advance,
> Best regards,
> João Henriques
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