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.
Hi ALL,
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)
Regards,
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