[gmx-users] .mdp file for polymer

Berk Hess gmx3 at hotmail.com
Mon Feb 16 11:47:41 CET 2009


You should be much more precise in describing your problems.
gmxdump does not seem to give a segv at all.
Also you did not mail me your Gromacs version.

mdrun immediately gives a warning:
Warning: 1-4 interaction between 1 and 28 at distance 0.982 which is larger than the 1-4 table size 0.500 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file

You seem to have reduced the table size from the default 1.0 to 0.5.
But if interactions are beyond the table size, you need to increase the table.

Also your cut-off's are 0.1 nm, which is much smaller than the size of your atoms.
This simulation setup is complete nonsens.
You can never expect a system to run propely with these kind of settings.


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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