[gmx-developers] genbox in git version 4.0.99_development_20090605

[Berk Hess]

Hi,

I have fixed this already, do a git pull.

Berk

Michel Cuendet wrote:
> Hi
>
> Note that all steps below work fine with version 4.0.4.
>
> I am trying to simulate one ion in water.  I start with a one-line pdb
> file ion.pdb:
>
> ATOM      1  NA  NA+     1       9.028  16.846  31.410  1.00  0.00
>
> And I do :
>
> echo 3 | pdb2gmx -f ion.pdb
> editconf -f conf.gro  -o -c -d 1.5 -bt triclinic
> genbox -cp out.gro -cs -p  -o solvated.gro
>
> [ ... tons of output ... ]
> Calculating Overlap...
> box_margin = 0.315
> Removed 1737 atoms that were outside the box
> Neighborsearching with a cut-off of 0.33
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw:     TRUE
> Cut-off's:   NS: 0.33   Coulomb: 0.33   LJ: 0.33
> System total charge: 0.000
> -------------------------------------------------------
> Program genbox, VERSION 4.0.99_development_20090605
> Source code file: ns.c, line: 2420
>
> Fatal error:
> One of the box vectors has become shorter than twice the cut-off
> length or box_yy-|box_zy| or box_zz has become smaller than the cut-off.
> For more information and tips for trouble shooting please check the
> GROMACS Wiki at
> http://wiki.gromacs.org/index.php/Errors
> -------------------------------------------------------
>
>
> Cheers,
>
> Michel
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