[gmx-developers] Bugs in g_sdf

Ondrej Marsalek ondrej.marsalek at gmail.com
Tue Oct 13 18:16:59 CEST 2009

Dear GROMACS developers,

I have recently started using the g_sdf (so far only in mode 1) and I
like it, but I have noticed two issues with it:

1) The refmol structure seems to be wrong if the reference groups are
longer than one. It does work with one reference molecule only. This
has been reported before:


2) The normalization of the SDF is wrong. It seems that (at least) the
number of frames is not accounted for properly. The absolute values of
the SDF grow with the number of frames used. Also, a brief look at the
code in src/tools/gmx_sdf.c suggests that the number of frames used is
not considered at all (all normalization is done with the variable

I would very much like to see these issues resolved. I'd be glad to
help, but am totally new to GROMACS on the coding side, so I can't
provide a patch, at least not now.

Best regards,
Ondrej Marsalek

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