[gmx-users] error while running mdrun

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Aug 31 22:31:32 CEST 2005

Hi Rahul,

That's a rather large box, measuring millimeters! And the vectors have 
negative signs on the diagonal elements, which is weird. Isn't your system 
exploding? I'd say something terribly wrong, but can't comment further 
without more information (grompp warnings?, energy minimization?).



On 8/31/05, Rahul Karyappa <r.karyappa at ncl.res.in> wrote:
> dear all gromacs-users ,
> This is very important for me. I really need your help to solve this 
> problem. I have to run MD on a 48 repeat units polymer surrounded by water 
> molecules in a box. For a test run I have taken MD parameters which are 
> given on the GROMACS website under .mdp file format option.
> When I ran the mdrun, it starts but as time progresses the size of the 
> md.log file keep increasing with the errors. One error type is like as 
> follows:
> Correcting invalid box:
> old box (3x3):
> old box[ 0]={-9.43863e+07, 0.00000e+00, -0.00000e+00}
> old box[ 1]={ 0.00000e+00, -9.43863e+07, -0.00000e+00}
> old box[ 2]={ 0.00000e+00, 9.91055e+09, -9.43863e+07}
> new box (3x3):
> new box[ 0]={-9.43863e+07, 0.00000e+00, -0.00000e+00}
> new box[ 1]={ 0.00000e+00, -9.43863e+07, -0.00000e+00}
> new box[ 2]={ 0.00000e+00, 1.00049e+10, -9.43863e+07}
> I have no idea what I can do. Please help me out.
> One more thing, when I ran mdrun for smaller no. of repeat units like 1,2 
> and 4 it ran successfully. Looking forward to your kind reply. Thanking you 
> in advance.
> Rahul Karyappa
> NCL, India
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciencesand Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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