Hi,
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.
Berk
Date: Mon, 16 Feb 2009 12:57:50 +0400
From: varsha.gautha...@gmail.com
To: gmx-users@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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