[gmx-users] .mdp file for polymer

varsha gautham varsha.gautham88 at gmail.com
Mon Feb 16 09:57:50 CET 2009


Hello sir,

On giving gmxdump its giving me an error saying "segmentation fault.My box
size is 6x6X6.Am trying to run it it vaccum for 250 ps wit 50000 timesteps
and with columb type=PME. I read from mailing list that PME calculations
requires large amount of memory space.Is this an issue with dimension of box
or with the system memory allocation ?Here's my log file.

T-Coupling  :     106  (total 106 atoms)
Energy Mon. :     106  (total 106 atoms)
Acceleration:     106  (total 106 atoms)
Freeze      :     106  (total 106 atoms)
User1       :     106  (total 106 atoms)
User2       :     106  (total 106 atoms)
VCM         :     106  (total 106 atoms)
XTC         :     106  (total 106 atoms)
Or. Res. Fit:     106  (total 106 atoms)
QMMM        :     106  (total 106 atoms)
ben-nch0.xtc frame 0:
   natoms=         1  step=         0  time=-2.9120485e-05  prec=2.8026e-45
   box (3x3):
      box[    0]={-2.89059e-05,  3.98821e-34, -2.39380e-05}
      box[    1]={ 3.98770e-34,  1.40130e-45, -2.91168e-05}
      box[    2]={-1.96789e+00, -2.91207e-05, -1.96789e+00}
   x (1x3):
Segmentation fault
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