[gmx-users] pbc doubt

Adriana Pietropaolo adriana at ms.fci.unibo.it
Thu Apr 6 14:47:09 CEST 2006

Hi all,
I have a doubt with the pbc applied in the MD.
I converted the xtc file in pdb with trjconv.
Checking with rasmol the pdb file, I found that the protein is always not 
broke in fragments and the box is always fix.
Subsequently, I tried to use the option -pbc whole, which breaks the 
protein in more fragments, but the box is always fix, not spanned.
I would like to analyze my gromacs trajectory making some codes written 
from my self, but I have this pbc doubt.
So, how can I remove the pbc from the xtc files? 
I think that for the protein in the xtc file pbc are already removed, 
but for the solvent are not removed.
Let me to ask another question:
Do you think that for the trajectory analysis with my fortran codes
I can use the format g96?
Thanks in advance,

Adriana Pietropaolo,
PhD student,
dipartimento di Chimica Fisica ed Inorganica,
Facolta' di Chimica Industriale
Universita' di Bologna
Tel 051/6446992
FAX 051/2093690 

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