On January 17, 2011 at 4:32 PM jojo J <[email protected]> wrote:
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
output.mdrun
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
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.
TJ Mustard
Email: [email protected]
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