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

Amin Arabbagheri amin_arab at yahoo.com
Sun Nov 14 08:01:55 CET 2010

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,

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101113/0b9ade66/attachment.html>

More information about the gromacs.org_gmx-users mailing list