simulation problems

From: baxy (baxy_at_hi.htnet.hr)
Date: Mon May 14 2007 - 16:42:44 CDT

I have just started using namd so I' still learning about simulations and using namd.

 

when i start simulation everything starts normally and then everything stops and message in log file appears:

 

 

...

BRACKET: 4.72686e-007 2862.2 -1.92737e+010 -1.17053e+010 -9.76173e+009
PRESSURE: 100 3.7681e+006 -43652 44676.8 -43652 3.80751e+006 79376.6 44676.8 79376.6 3.66871e+006
GPRESSURE: 100 3.97243e+006 -32857.6 36805.4 -64533 4.01785e+006 96165.2 73970.8 100880 3.84696e+006
Info: Initial time: 1 CPUs 1.65438 s/step 9.57396 days/ns 0 kB memory
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG

 

ENERGY: 100 143355.9983 15787.4667 247.2572 114.3492 -20398.7584 1181867.5228 0.0000 0.0000 0.0000 1320973.8358 0.0000 1320973.8358 1320973.8358 0.0000 3748109.5319 3945747.4231 86856.0000 3748109.5319 3945747.4231

 

REINITIALIZING VELOCITIES AT STEP 100 TO 310 KELVIN.
TCL: Running for 3000 steps
ERROR: Constraint failure in RATTLE algorithm for atom 25!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 63!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 78!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 124!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 5!
ERROR: Constraint failure; simulation has become unstable.

 

 

appears. what is the problem??

 

robert

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