[gmx-users] unexpected result from mdrun

[David Mobley]

Maybe they're not exactly identical? Did you try gmxdump and then diff
the output?

David

On 6/19/06, Dongsheng Zhang <dong at pampas.chem.purdue.edu> wrote:
> 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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