From: Satyavani Vemparala (vani_at_VITAE.CMM.UPENN.EDU)
Date: Sun Mar 21 2004 - 20:23:33 CST
Hi:
Iam doing a simulation where a part of the system is held fixed. iam first
trying to minimize the system for 2000 steps. This is the output at the
end of minimization :
PRESSURE: 2000 -1389.26 -78.8149 859.158 748.736 -877.249 -2159.74 12.3179
39.7088 -1388.94GPRESSURE: 2000 -1324.02 -106.593 854.279 720.234 -806.813
-2156.96 10.6098 9.65437 -1454.73ETITLE: TS BOND
ANGLE DIHED IMPRP ELECT VDW
BOUNDARY MISC KINETIC TOTAL TEMP
TOTAL2 TOTAL3 TEMPAVG PRESSURE GPRESSURE
VOLUME PRESSAVG GPRESSAVG
ENERGY: 2000 22813.2510 5509.8530 2096.0492
17.1025 -27321.4107 118669.5085 0.0000 0.0000
11257.5563 133041.9098 305.8062 133052.8315
133011.8753 305.8062 -1218.4816 -1195.1885
363520.0000 -1218.4816 -1195.1885
After the minimization, i submit again for run, and at the first step,
this is the output:
PRESSURE: 2000 nan nan nan nan nan nan nan nan nan
GPRESSURE: 2000 nan nan nan nan nan nan nan nan nan
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
KINETIC TOTAL TEMP TOTAL2 TOTAL3
TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG
GPRESSAVG
ENERGY: 2000 22813.2516 5509.8527 2096.0493
17.1025 -27321.4107 118669.5080 0.0000 0.0000
-99999999.9999 -99999999.9999 -99999999.9999 -99999999.9999
-99999999.9999 -99999999.9999 -99999999.9999 -99999999.9999
363520.0000 -99999999.9999 -99999999.9999
I don't understand this huge increase in pressure. might be because of
rattle, but i don't know how to stop the simulation from crashing!!
The following is the error:
OPENING EXTENDED SYSTEM TRAJECTORY FILE
ERROR: Margin is too small for 9 atoms during timestep 2001.
ERROR: Incorrect nonbonded forces and energies may be calculated!
Any suggestions?
Thanks
Vani
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