[gmx-users] 1-4 interaction, a distance greater than table size
Justin A. Lemkul
jalemkul at vt.edu
Sun Nov 14 13:26:30 CET 2010
Amin Arabbagheri wrote:
> 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.
A complete .mdp file would be significantly more useful. Did you do energy
minimization? If so, what was the outcome?
> Thanks in advance for any instruction,
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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