[gmx-users] unexpected result from mdrun

[Dongsheng Zhang]

Dear GMX users,

I have two EXACTLY identical tpr files at two different directories on
the SAME machine. When I try to use these two tpr files. One works fine.
Another one gives me bad result, the molecule explodes. Could anyone
tell me why this happens? Thank you in advance!


Dongsheng

On Mon, 2006-06-19 at 14:52 -0400, Dongsheng Zhang wrote:
> Dear GMX users,
> 
> I am studying the interaction between a polymer chain and a nanotube in
> vacuum. After I set up my system, I use vmd to visualize my gro file. It
> looks fine. The polymer chain is a little far away from the nanotube.
> There is no overlap. However, after I do mdrun, I can't get edr file
> (empty). The log file is as follows:
> 
> 
> 
> There are 1008 atoms in your xtc output selection
> 
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
> Molecular dynamics with coupling to an external bath
> J. Chem. Phys. 81 (1984) pp. 3684-3690
> -------- -------- --- Thank You --- -------- --------
> 
>    Energies (kJ/mol)
>            Bond          Angle       G96Angle Ryckaert-Bell.
> LJ-14
>     9.09629e+02    4.91326e+02    2.36889e+01    2.32269e+03    3.46380e
> +04
>      Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic
> En.
>     9.42152e+02    3.60034e+03   -1.16196e+03    4.17659e+04    3.97332e
> +05
>    Total Energy    Temperature Pressure (bar)
>     4.39097e+05    3.16685e+04    0.00000e+00
> 
> Large VCM(group rest):     -0.07615,      0.03311,      0.00164,
> ekin-cm:  3.72526e+01
> Group rest with mass  1.08005e+04, Ekrot  6.72960e+03 Det(I) =  1.33951e
> +29
>   COM:      0.07250       0.17529       1.86474
>   P:     -822.48108     357.63647      17.73926
>   V:       -0.07615       0.03311       0.00164
>   J:   -1438767104.00000  -38931256.00000  -906993664.00000
>   w:        0.00004      -0.00004      -0.00007
> Inertia tensor (3x3):
>    Inertia tensor[    0]={ 5.38545e+13, -4.65369e+13, -8.34326e+13}
>    Inertia tensor[    1]={-4.65369e+13,  4.02137e+13,  7.20962e+13}
>    Inertia tensor[    2]={-8.34326e+13,  7.20962e+13,  1.29256e+14}
> Large VCM(group rest):      0.01199,     -0.09814,      0.04721,
> ekin-cm:  6.48211e+01
> Group rest with mass  1.08005e+04, Ekrot  6.62037e+04 Det(I) =  5.30238e
> +28
>   COM:      0.07266       0.17504       1.86508
>   P:      129.52625   -1059.92761     509.88013
>   V:        0.01199      -0.09814       0.04721
>   J:   -4924144128.00000  220606032.00000  -3301491456.00000
>   w:        0.00072      -0.00064      -0.00116
> Inertia tensor (3x3):
>    Inertia tensor[    0]={ 5.54846e+13, -4.79487e+13, -8.59614e+13}
>    Inertia tensor[    1]={-4.79487e+13,  4.14364e+13,  7.42863e+13}
>    Inertia tensor[    2]={-8.59614e+13,  7.42863e+13,  1.33179e+14}
> Large VCM(group rest):      0.06178,     -0.00576,      0.03008,
> ekin-cm:  2.56742e+01
> Group rest with mass  1.08005e+04, Ekrot  3.70064e+03 Det(I) = -4.14226e
> +27
>   COM:      0.07271       0.17515       1.86534
>   P:      667.20703     -62.18475     324.89392
>   V:        0.06178      -0.00576       0.03008
>   J:   -564741376.00000  -1195921280.00000  302564480.00000
>   w:        0.00016      -0.00015      -0.00026
> 
> 
> I have seen that LJ (SR) is positive. I believe something is wrong here.
> Could anyone give me a hint what's happening? Thank you very much.
> 
> 
> All the best!
> 
> Dongsheng
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