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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