[gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

Justin A. Lemkul jalemkul at vt.edu
Wed Nov 17 19:48:01 CET 2010

X Rules wrote:
>  > The error would imply that the box you have set up is < 2.0 nm, given 
> the
>  > cutoffs here. How did you define the box (editconf command)? What is 
> your box
>  > size (last line of the .gro file or in the header of a .pdb)?
>  >
>  > -Justin
> okey.. I got it under control. The problem was.
> 1. created a good box widths.. went upto 30nm with editconf and box vector
> 2. (Made a mistake while adding ions with genion): *saved the file as 
> pdb instead of gro!!*
> 3. was trying grompp with the pdb file (So I have no idea what grommp 
> found different in a file with/witout ions)
> Thanks for hinting on the last line of gro. (still I think it is 
> probably a bug or feature)

There was a bug in an early 4.0.x feature that box vectors were not properly 
written to .pdb files (CRYST line), but this was obviously fixed months, if not 
a year or more, ago.  Gromacs tools are expected to handle numerous file types 
effortlessly, so using .gro is certainly not required.  If you have direct 
evidence that some tool has written or interpreted the box incorrectly, then 
please file a bugzilla, but otherwise something else likely went wrong.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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