[gmx-users] mdrun: broken molecules?

[Perttu Niemelä]

Dear gmx-users,

Is it true that mdrun (3.3.1) should not write broken
molecules under any circumstances? If the .xtc output
contains broken molecules, should one be worried?

The molecules in my .xtc file are whole for the most of the
time, but at some frames one or two are broken such that parts
of the molecule are on opposite sides of the periodic box. I
checked this with gmxdump and a short code of my own. Also,
I was not able to make the molecules whole again with any of
the -pbc options in trjconv. The molecules in the initial
configuration are whole and I cannot see any reason for this.

Best Regards,

Perttu Niemela
Helsinki Univ. Tech.
Finland