[gmx-users] segmentation fault

[Dongsheng Zhang]

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