VMD-L Mailing List

From: Bogdan Costescu (bcostescu_at_gmail.com)
Date: Tue Jul 24 2012 - 11:39:55 CDT

On Tue, Jul 24, 2012 at 3:19 PM, Bogdan Costescu <bcostescu_at_gmail.com> wrote:
> It seems to me that the VMD
> reader plugin assumes that the format is "%7.3f"

I was partly wrong: it's "%f"...

> and that there is a
> separator character between the different coordinate columns.

... but I was also partly right: it's " %f" (note the space before %f) :)

The format is defined on line 1060, in gro_rec():

http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/Gromacs_8h-source.html#l01048

where the last 3 items are the coordinates, read as " %f %f %f".
Compare this with the GROMACS code writing them:

> The writing for GRO files is done in write_hconf_indexed_p() with
> "%8.3f%8.3f%8.3f"

So there is indeed a mismatch. You found a bug in the GROMACS reader plugin :)

Cheers,
Bogdan