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

--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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