Dear All,
I'm simulating a DNA duplex using amber99p. starting the simulation(step 0) i
face an error which tells:
starting mdrun 'Protein in water'
500000 steps, 500.0 ps.
step 0Warning: 1-4 interaction between 136 and 179 at distance 96871502.536
which is larger than the 1-4 table size 2.000 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
or with user tables increase the table size
Segmentation fault
I've checked the distance between atoms 136 and 179, its quite normal, about 3
angstrom (not 96871502 !!).
Im also attaching the output (md.log) which may help finding a reason:
Started mdrun on node 0 Sun Nov 14 10:17:10 2010
Step Time Lambda
0 0.00000 0.00000
Grid: 9 x 9 x 9 cells
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
1.77478e+02 6.08613e+02 1.86464e+02 1.58123e+03 6.34721e+02
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
-1.03292e+04 4.16184e+04 -3.45397e+05 -3.54920e+04 -3.46412e+05
Kinetic En. Total Energy Temperature Pressure (bar)
5.24527e+01 -3.46359e+05 2.90932e-01 -6.00103e+03
Maybe its necessary to say that, I'm coupling my system with both thermostat
and barostat, using a reasonable temperature of 300K.
Thanks in advance for any instruction,
Amin
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