[gmx-users] infinite CNT and segmentation fault

[Vitaly Chaban]

Hello,

I try to simulate infinite nanotube.

The bonds in topology are as follows:
    1     2     1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05
    1    31     1  1.400000e-01  4.000000e+05  1.400000e-01  4.000000e+05 
    1  1500     1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05 
    2    32     1  1.440000e-01  4.000000e+05  1.440000e-01  4.000000e+05 
    2  1471     1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05 
    3     4     1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05 
    3    33     1  1.400000e-01  4.000000e+05  1.400000e-01  4.000000e+05 
    3  1472     1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05 
    4    34     1  1.440000e-01  4.000000e+05  1.440000e-01  4.000000e+05 
    4  1473     1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05 
..........................................................................
..........................................................................

The coordinates:
    1UNK      C    1   2.312   3.095   0.071
    1UNK      C    2   2.448   3.055   0.071
    1UNK      C    3   2.698   2.922   0.071
    1UNK      C    4   2.807   2.831   0.071
    1UNK      C    5   2.982   2.607   0.071
    1UNK      C    6   3.044   2.480   0.071
    1UNK      C    7   3.112   2.205   0.071
    1UNK      C    8   3.117   2.063   0.071
............................................
............................................
    1UNK      C 1495   1.305   2.735   6.101
    1UNK      C 1496   1.511   2.929   6.101
    1UNK      C 1497   1.633   3.003   6.101
    1UNK      C 1498   1.900   3.097   6.101
    1UNK      C 1499   2.041   3.115   6.101
    1UNK      C 1500   2.323   3.092   6.101
   4.20000   4.20000   6.17200


The output of mdrun:
Back Off! I just backed up md.log to ./#md.log.2#
Getting Loaded...
Reading file topol.tpr, VERSION 3.3.1 (single precision)
Loaded with Money


Back Off! I just backed up ener.edr to ./#ener.edr.2#
starting mdrun 'ICE'
1000 steps,      0.0 ps.

Segmentation fault

The distances between images seem to be correct. pbc=full in mdp.
Pressure coupling is off. If one runs x2top without '-pbc' everything is
OK.
What else can be wrong?

Can the below warning lead to the crash (grommp):
WARNING 2 [file aminoacids.dat, line 1]:
  Can not exclude the lattice Coulomb energy between energy groups
Checking consistency between energy and charge groups...

How to overcome it?

Thanks.

-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
skype: vvchaban
tel.: +38-097-8259698