From: Ugur Akgun (ugur_iowa_at_hotmail.com)
Date: Mon Feb 26 2007 - 16:32:24 CST
Hi All;
I have a water, protein, and CO2 system. The system successfully minimizes
but at the first step of MD equilibration it gives the error I pasted below.
Let me summarize what i did to debug this;
- I don't use useFlexibleCell feature, but when I added "useFlexibleCell no"
to the input file.. Doing this does not change the error.
- I put a term "margin 2.5" and I changed it up to 8... still the same
error...
- The water, protein, lipid system equilibrates successfully, The problem
comes from CO2..
- I believe it is CO2 parameter file, I'd really appreciate any ideas, and a
nice CO2 parameter file..
thanks a lot
cheers
ugur akgun
ETITLE: TS BOND ANGLE DIHED IMPRP
ELECT VDW BOUNDARY MISC
KINETIC TOTAL TEMP TOTAL2 TOTAL3
TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG
GPRESSAVG
ENERGY: 0 13188.8073 18461.4224 12561.1557 129.1724
-413297.4367 10436.7914 0.0000 0.0000
99999999.9999 99999999.9999 99999999.9999 99999999.9999
99999999.9999 99999999.9999 99999999.9999 99999999.9999
1408176.0000 99999999.9999 99999999.9999
ERROR: Margin is too small for 9 atoms during timestep 1.
ERROR: Incorrect nonbonded forces and energies may be calculated!
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
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