[gmx-users] Regarding the 'hangs at "atom 0"' issue with x2top 4.x

Vasilii Artyukhov darth.vasya at gmail.com
Wed Aug 5 01:46:45 CEST 2009

Hi all,

I've recently managed to reproduce the bug with x2top 4.x hanging at "atom
0". The halt occurred when I was trying to generate a topology with the
"-pbc yes" option (which is the default used unless you specify otherwise)
using a structure file containing no information on the periodic box. As
soon as I added the box info, x2top 4.0.4 did successfully generate a
topology for me.

I'm using x2top for periodic molecules (just forgot to add the box string
this one time), so I didn't bother actually trying to turn off PBC, but I
strongly suspect that this is the actual source of the problem reported by
many colleagues on the list. Perhaps someone who previously complained about
x2top 4.x halting should try first adding the -nopbc option to their command
line and then adding the box vectors to their .gro and tell us all what
happens then! :) Also, the developers might want to consider doing something
about this setting and its default value.

Aside from this one time, I've never had any problems with x2top 4.0.4
(especially with the -noparam option that I use all the time, just to keep
things simple), and its value at generating topologies for my 2D periodic
molecules cannot be overemphasized :)

Hope this helps someone,
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