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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