[gmx-users] (no subject)

[K.A. Feenstra]

"nicolis at guideo.fr" wrote:
> 
> Sorry my mail server had problems so I post again.
> 
> Hello,
> I reply with a copy to the list because I have problems equilibrating the box.
> Actually, it "looks" equilibrated. I mean that I begin a 1ns simulation and for
> the first 221690 steps (1fs each, so the first 221.69p
> s) the density, temperature, energies (KE, PE, LJ, Coulomb, dispersion, LR
> etc), volume, x,y,z, of the box seam stable oscillating aro
> und reasonable values. Looking at the ngmx animation, everything looks fine
> as well. But then, after step 221690 I get a crash. Here i
> s the output:
> 
> ********************begin mdrun output**************
> 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.
> 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.
> 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.
> Warning: Only triclinic boxes with the first vector parallel to the!
>  x-axis an
> d 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.
> 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.
> 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.
> Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 210]
> ********************end mdrun output**************
> Of course I looked at the box size but at the last recorded step it is OK. Any
> ideas, suggestions, help?

Have you looked at the properties of the last 'normal' step, i.e. the
step just before the box went NaN? You might not have that data, since
you probably only store energies every 1ps or so, but if the problem
is reproducible (as Eric already asked), you could re-run from just 
before the crash and output every step to energy file.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "If You See Me Getting High, Knock Me Down"               |
|        | (Red Hot Chili Peppers)                                   |
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