[gmx-users] 1-4 interaction, a distance greater than table size

[Justin A. Lemkul]

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?

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

> Thanks in advance for any instruction,
> Amin
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================