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On January 17, 2011 at 4:32 PM jojo J <joojoojooon@gmail.com> wrote:<br />
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Dear users,<br />
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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 />
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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 />
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NOTE 1 [file md.mdp]:<br />
  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting<br />
  nstcomm to nstcalcenergy<br />
<br />
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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 />
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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 />
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output.mdrun<br />
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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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<p style="margin: 0px;">I seem to have a similar problem but you are having many more than I. If I were you I would fix the two "NOTES" first. Once those go away the 1-4 interaction warning might disappear as well.</p>
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<p style="font-family: monospace; white-space: nowrap; margin: 5px 0px 5px 0px;">TJ Mustard<br />
Email: mustardt@onid.orst.edu</p>
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