[gmx-users] unexpected result from mdrun

[Dongsheng Zhang]

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