[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 21:28:00 CET 2010

X Rules wrote:
>  >
>  > 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
> well I will check a bit more and submit it to bugzila as there is no 
> cryst line if you write a pdb with genion .. so that might be the root 
> cause to my problems.

I would investigate that very thoroughly and be very sure it's reproducible 
before submitting a bugzilla.  I've run through an entire workflow (pdb2gmx, 
editconf, genbox, genion, grompp, mdrun) with lysozyme using both .gro and .pdb 
files and everything works fine either way.  That doesn't preclude the 
possibility of a bug somewhere, but I would think it very unlikely that a bug 
exists in something so fundamental that was fixed a very long time ago.



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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