[gmx-users] table-extension in mdp ?!

jojo J joojoojooon at gmail.com
Tue Jan 18 01:32:22 CET 2011

Dear users,

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.

Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'solute'
Velocities were taken from a Maxwell distribution at 300 K
Number of degrees of freedom in T-Coupling group System is 8685.00

NOTE 1 [file md.mdp]:
  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
  nstcomm to nstcalcenergy

NOTE 2 [file md.mdp]:
  The sum of the two largest charge group radii (0.204120) is larger than
  rlist (1.100000) - rvdw (1.000000)

Analysing residue names:
There are:   240      Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Largest charge group radii for Van der Waals: 0.102, 0.102 nm
This run will generate roughly 343 Mb of data


step 7200, will finish Tue Jan 18 03:51:24 2011imb F  9%
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
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
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