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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