[gmx-users] mdrun problems

[David]

On Tue, 2004-05-11 at 21:30, Scott Classen wrote:
> Hello GROMACS Users,
> I am attempting to perform MD on a small molecule in a box of DMSO and 
> after a few cycles of the simulation my log file starts growing very 
> rapidly (Ikilled the job when my log file ballooned to 1GB). The file 
> is mostly full of lines such as these:
> 
> Correcting invalid box:
> old box (3x3):
>     old box[    0]={-1.47359e+04,  0.00000e+00, -0.00000e+00}
>     old box[    1]={ 0.00000e+00, -1.47827e+04, -0.00000e+00}
>     old box[    2]={ 0.00000e+00,  1.18314e+09, -1.58862e+04}
> new box (3x3):
>     new box[    0]={-1.47359e+04,  0.00000e+00, -0.00000e+00}
>     new box[    1]={ 0.00000e+00, -1.47827e+04, -0.00000e+00}
>     new box[    2]={ 0.00000e+00,  1.18316e+09, -1.58862e+04}
> Correcting invalid box:
> old box (3x3):
>     old box[    0]={-1.47359e+04,  0.00000e+00, -0.00000e+00}
>     old box[    1]={ 0.00000e+00, -1.47827e+04, -0.00000e+00}
>     old box[    2]={ 0.00000e+00,  1.18316e+09, -1.58862e+04}
> new box (3x3):
>     new box[    0]={-1.47359e+04,  0.00000e+00, -0.00000e+00}
>     new box[    1]={ 0.00000e+00, -1.47827e+04, -0.00000e+00}
>     new box[    2]={ 0.00000e+00,  1.18317e+09, -1.58862e+04}
> Correcting invalid box:
> old box (3x3):
>     old box[    0]={-1.47359e+04,  0.00000e+00, -0.00000e+00}
>     old box[    1]={ 0.00000e+00, -1.47827e+04, -0.00000e+00}
>     old box[    2]={ 0.00000e+00,  1.18317e+09, -1.58862e+04}
> 
> 
> Any ideas what I may be doing wrong?
IIRC you had a triclinic box. Any special reason for that, like
simulating a crystal? Otherwise it may be that your pressure scaling is
too tight (make tau_p larger). 

Which gromacs version?


> Thanks in advance,
> Scott
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>    Scott Classen, Ph.D.
>    ACS Postdoctoral Fellow
>    Department of Molecular & Cell Biology
>    University of California, Berkeley
>    237 Hildebrand Hall #3206
>    Berkeley, CA 94720-3206
>    LAB 510.643.9491
>    FAX 510.643.9290
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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