error messages with "reinitvels"

From: Yinglong Miao (yimiao_at_indiana.edu)
Date: Fri Jun 20 2008 - 13:56:25 CDT

Dear NAMDers,

I have been getting error messages with "reinitvels" in running NAMD. In the
simulation, a 2ns NPT ensemble equilibration has been run before calling
"reinitvels" to reinitializing atomic velocities. The simulation outputs
"nan" for the temperature, kinetic and total energies, even though the
temperature is kept the same. Also the ELECT and VDW energies are found to
be different after the velocity reinitialization, which doesn't make sense,
because it's still the same structure. The error messages are pasted below.
Any of your suggestions will be greatly appreciated.

~~~~~~~~~~~~~~~~~~~~~

ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
TOTAL2 TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG

ENERGY: 2000100 181602.9833 290908.0145 178686.8571
16883.4971 -10018869.7640 653684.9962 0.0000
0.0000 1845959.4396 -6851143.9763 296.9132 -6844757.9090
-6844724.9098 296.9132 -17884.5371 -6.0203
27825251.6784 -17884.5371 -6.0203

REINITIALIZING VELOCITIES AT STEP 2000100 TO 298.15 KELVIN.
TCL: Setting parameter firsttimestep to 2000100
TCL: Running for 100 steps
..
ERROR: Atom 8695 velocity is 1.37246e+06 -717578 -254249 (limit is 10000)
ERROR: Atom 195906 velocity is 119305 7192.23 -615018 (limit is 10000)
ERROR: Atoms moving too fast; simulation has become unstable.
..
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
TOTAL2 TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG

ENERGY: 2000100 181602.9996 290908.0218 178686.8560
16883.4910 -9898313.0351 99999999.9999 0.0000
0.0000 nan nan nan
nan nan nan nan nan
27825196.0229 nan nan

~~~~~~~~~~~~~~~~~~~~~

Thanks,

-- 
Yinglong Miao
Ph.D. Candidate
Center for Cell and Virus Theory
Chemistry Department, Indiana University
800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
Tel: 1-812-856-0981

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