[gmx-users] Only triclinic boxes

[Anton Feenstra]

Rahul Banerjee wrote:
> Dear Gromacs users,
> 		I am getting a strange error when I run mdrun
> program for MD. It says,
> Warning: Only triclinic boxes with the first vector
> parallel to the x-axis and the second vector in the
> xy-plane are supported.
>  Box (3x3):
>  Box[    0]={         nan,          nan,          nan}
>  Box[    1]={         nan,          nan,          nan}
>  Box[    2]={         nan,          nan,          nan}
>          Can not fix pbc.
> 
> Afer that program ends due to Segmentation 
> Although during Energy Minimisation step this warings
> do not occur. Can you please tell me why so happens
> and also how to overcome this?

This is one of the possible symptoms of an exploding system.
You don't see it during EM, because there is no pressure coupling.
You will need to examine your starting structure for bad contacts,
strange conformation etc. and find a way to get rid of them.
Doing more EM might help, taking more cautious steps during
building your system might help, too.

You might consider adopting my general startup procedure for
a protein (+ possible crystal waters and ligand) in water:
1) minimize protein (+crystal water + ligand) in vacuum
2) add water (genbox), and ions if you want & need them
3) minimize protein + solvent
4) short md (1 ps or so) with position restraints on heavy atoms
    of Protein (and crystal waters and ligand)
5) 'production run'



-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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