CVS mdrun writes broken molecules when using -dd
when using domain decomposition, the CVS mdrun writes broken molecules. E.g.,
mpirun C mdrun_cvs -v -dd 2 2 1 -s topol.tpr # topol.tpr is for 4 nodes
trjconv -s topol.tpr -f traj.xtc -dump 0.01 -o out.pdb
Gives an out.pdb with atoms inside the box. Using -pbc whole (actually, this is a different bug)
trjconv -s topol.tpr -f traj.xtc -pbc whole -o whole.pdb -dump 0.01
does not help.
Regards from Goettingen,
(The Attached tpr is made for 4 nodes and runs only 10 steps.)
#3 Updated by Jochen Hub over 12 years ago
(In reply to comment #2)
This is not a bug, but a consequence of the fact that there is no global graph
when we apply domain decomposition. We'll update the documentation that says
"gromacs doesn't write broken molecules" before we release 4.0, though.
Hi Erik, thanks for the quick reply. If from now on mdrun places all atoms in the box it would, however, be good if the "-pbc whole" and/or "-pbc com" options of trjconv would work. In my case, none of them changed the output of trjconv:
trjconv -f traj.xtc -o com.pdb -pbc com -s topol.tpr -dump 0.01
trjconv -f traj.xtc -o whole.pdb -pbc whole -s topol.tpr -dump 0.01
Here, in both com.pdb and whole.pdb all atoms are inside the box.