<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear All,<br><br>I'm simulating a DNA duplex using amber99p. starting the simulation(step 0) i face an error which tells:<br><br><div style="margin-left: 40px;">starting mdrun 'Protein in water'<br></div><div style="margin-left: 40px;">500000 steps, 500.0 ps.<br>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<br>These are ignored for the rest of the simulation<br>This usually means your system is exploding,<br>if not, you should increase table-extension in your mdp file<br>or with user tables increase the table size<br>Segmentation fault<br></div><br>I've checked the distance between atoms 136 and 179, its quite normal, about 3 angstrom (not 96871502 !!). <br>Im also attaching the output (md.log) which may help finding a reason:<br><br><div style="margin-left:
40px;">Started mdrun on node 0 Sun Nov 14 10:17:10 2010<br><br> Step Time Lambda<br> 0 0.00000 0.00000<br><br>Grid: 9 x 9 x 9 cells<br> Energies (kJ/mol)<br> Bond Angle Proper Dih. Ryckaert-Bell. LJ-14<br> 1.77478e+02 6.08613e+02 1.86464e+02 1.58123e+03 6.34721e+02<br> Coulomb-14 LJ
(SR) Coulomb (SR) Coul. recip. Potential<br> -1.03292e+04 4.16184e+04 -3.45397e+05 -3.54920e+04 -3.46412e+05<br> Kinetic En. Total Energy Temperature Pressure (bar)<br> 5.24527e+01 -3.46359e+05 2.90932e-01 -6.00103e+03<br><br></div>Maybe its necessary to say that, I'm coupling my system with both thermostat and barostat, using a reasonable temperature of 300K.<br><br>Thanks in advance for any instruction,<br>Amin<br></td></tr></table><br>