[gmx-users] .mdp file for polymer

Berk Hess gmx3 at hotmail.com
Mon Feb 16 10:15:07 CET 2009


Independent of any other problems you might have, gmxdump should never give a segmentation fault.

Could you mail me the tpr file?
Which version of Gromacs are you using?


Date: Mon, 16 Feb 2009 12:57:50 +0400
From: varsha.gautham88 at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] .mdp file for polymer

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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