Dear GMX users,
My system is PEO-PPO-PEO triblock polymers with a coarse grained force
field. The nonbonded interactions are tabulated. The interaction range
in my tables in 5 nm. The cutoff is 1.4 nm. The table extention is 2 nm.
If I simulation only one chain, it works fine. However, the program gave
me "Segmentation fault" when I simulated 30 chains. The log file seems
fine, as follows:
Step Time Lambda
5000 10.00000 0.00000
Energies (kJ/mol)
Bond Angle LJ-14 Coulomb-14 LJ
(SR)
1.10604e+04 2.16255e+04 3.01743e+02 6.81742e+01 -1.29044e
+05
Coulomb (SR) Potential Kinetic En. Total Energy
Temperature
0.00000e+00 -9.59881e+04 2.95806e+04 -6.64076e+04 2.99508e
+02
Pressure (bar)
8.75619e+00
Step Time Lambda
6000 12.00000 0.00000
Energies (kJ/mol)
Bond Angle LJ-14 Coulomb-14 LJ
(SR)
1.17095e+04 2.20613e+04 2.40772e+02 6.78325e+01 -1.31923e
+05
Coulomb (SR) Potential Kinetic En. Total Energy
Temperature
0.00000e+00 -9.78433e+04 2.96119e+04 -6.82314e+04 2.99825e
+02
Pressure (bar)
4.47005e+00
The program stopped at step 6990 without any error message.
When I ran the program with -debug, I got a different log file, as
follows:
++++ 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 --- -------- --------
Large VCM(group rest): -0.00000, -0.00000, 0.00000,
ekin-cm: 3.11775e-21
Energies (kJ/mol)
Bond Angle LJ-14 Coulomb-14 LJ
(SR)
1.00042e+04 1.01454e+04 1.36360e+03 6.50650e+00 -2.68845e
+04
Coulomb (SR) Potential Kinetic En. Total Energy
Temperature
0.00000e+00 -5.36480e+03 2.96549e+04 2.42901e+04 3.00260e
+02
Pressure (bar)
-2.46133e+01
Large VCM(group rest): -0.00000, -0.00000, 0.00000,
ekin-cm: 2.79878e-21
The program stopped at step 3600, and there is no output for step 1000,
2000 3000 even though I set nstlog = 1000 in my mdp file.
With -debug, I got three of ctab.xvg dtab.xvg, rtab.xvg, and one of
ctab14.xvg dtab14.xvg, rtab14.xvg. In table_*_*.xvg, I only use C6 term,
three dtab.xvg matches my input table_*_*.xvg. ctab.xvg and rtab.xvg
should be zeros, but I find some large negative values in the last
several line as follows:
#ctab.xvg.1 (for PEO-PEO COUL term)
3.3980000953e+00 -2.5368847225e+15 -5.3233641970e+22
3.3984000953e+00 -4.4703197993e+22 -2.2346273246e+26
3.3988000953e+00 -1.7877019745e+23 -4.4687222761e+26
3.3992000953e+00 -4.0220100090e+23 -6.7028177811e+26
3.3996000954e+00 -7.1499560834e+23 -8.9369125481e+26
#rtab.xvg.1 (for PEO-PEO C12 term)
3.3980000953e+00 -3.0786326528e+10 9.1349993896e+02
3.3984000953e+00 -3.0786326528e+10 1.0232022095e+03
3.3988000953e+00 -3.0786326527e+10 1.3522044678e+03
3.3992000953e+00 -3.0786326527e+10 1.9005067139e+03
3.3996000954e+00 -3.0786326526e+10 2.6681091309e+03
These are the only things I find specious. Could you please help me to
found what causes segmentation fault?
All the best!
Dongsheng
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