[gmx-users] Extend water layer along negative Z-direction

Chris Neale chris.neale at utoronto.ca
Mon Jun 1 15:18:04 CEST 2009

Hi Anirban,

I suspect that your problem is that you define a box with zero x, zero y, and a negative z. I think it's time to read the manual.


Thanks a lot Chris, Justin and Tsjerk for yor replies.
Actually, my problem is not fully resolved. A portion of the protein tail is outside the water box in the Z direction (coordinate in Z is -35). So as suggested by you when I am issuing the command "editconf -f box.gro -o BOX.gro -box 0 0 -3.5", but after that genbox is giving the error:

Fatal error:
Undefined solute box.
Create one with editconf or give explicit -box command line option

Please can you specify the proper command, so that the water box is extended only in the negative Z direction (to solvate the portion of the protein out of the box)


More information about the gromacs.org_gmx-users mailing list