[gmx-developers] genbox in git version 4.0.99_development_20090605

Michel Cuendet michel.cuendet at isb-sib.ch
Thu Aug 6 11:41:16 CEST 2009


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 




Michel Cuendet, Ph.D
Molecular Modelling Group
Swiss Institute of Bioinformatics
CH-1015 Lausanne, Switzerland

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