Dear users,<br><br>Please help me with the following problem. My simulation is crashing for an unstability reason I guess. Can you please help me what wrong is exaclty. I had done the simulation with exactly the same input files but with version 4.0.7 and never got this error. Thanks for your comments.<br>
<br><br>Generating 1-4 interactions: fudge = 0.5 <br>Generated 332520 of the 332520 1-4 parameter combinations <br>Excluding 3 bonded neighbours molecule type 'solute' <br>Velocities were taken from a Maxwell distribution at 300 K<br>
Number of degrees of freedom in T-Coupling group System is 8685.00 <br><br><br>NOTE 1 [file md.mdp]:<br> nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting<br> nstcomm to nstcalcenergy<br><br><br>
NOTE 2 [file md.mdp]: <br> The sum of the two largest charge group radii (0.204120) is larger than<br> rlist (1.100000) - rvdw (1.000000)<br><br>Analysing residue names:<br>There are: 240 Other residues<br>Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...<br>
Largest charge group radii for Van der Waals: 0.102, 0.102 nm <br>This run will generate roughly 343 Mb of data<br><br>output.mdrun<br><br>step 7200, will finish Tue Jan 18 03:51:24 2011imb F 9%<br>step 7300, will finish Tue Jan 18 03:44:57 2011Warning: 1-4 interaction between 2121 and 2128 at distance 12.290 which is larger than the 1-4 table size 2.100 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>
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