[gmx-users] regarding editconf

[Ali Khodayari]

Dear users,

 

I am trying to reorient and re-center my solute using editconf. Performing
such I can place the structure at the desired place, yet it is outside the
box when I visualize it in VMD. It leads to an error after mdrun complaining
about a water molecule not being settled. 

Here is the command I use:

$ gmx editconf -f cell.gro -o cell_newbox.gro -princ -bt triclinic -c
-center 0 0 0 -rotate 0 350 0 -n ndx.ndx

Do you see where the problem is?

Regards,

Ali