[gmx-users] "wrong" starting structure

[Andrea Carotti]

Hi gmx-users,
    I've performed a 18ns MD of a protein. Everything gone fine and now i'm
analyzing it.
The starting structure is partially diffused out of the box and when i
use -pbc nojump the output traj. comes with a chain in a box and the other
chain in another box so in vmd i have the protein "virtually splitted". I've
tried also to give as ref. structure a frame with the protein all in a
single box doing:
trjconv -f output.trr -o xxx.trr -s right_conf.gro -pbc nojump
(the so called "reference structure" is that of the option -s?...)
but nothing changed..what I'm doing wrong?
Please help me
TNX
Andrea


------------
Andrea Carotti
Dip. Farmaco-chimico (Università di Bari)
via E. Orabona, 4 ## CAP 70124 ## BARI (Italy)
web: http://www.farmchim.uniba.it/samba/
phone: (+39) 080 5442551  ##   fax: (+39) 080 5442230