From: MEHRAN MB (mb.mehran1_at_gmail.com)
Date: Fri May 31 2013 - 11:33:03 CDT
*Hi everyone,
*
*
*
*I am trying to pull one end of my protein while the other end is fixed;
But as soon as it starts dynamic (right after energy minimization) and i
get this error:
ERROR: Constraint failure in RATTLE algorithm for atom 5!
ERROR: Constraint failure; simulation has become unstable.
*
*it always happen for atom 5 or 7, please note that I am fixing atom 5 (CA)
which is bonded to atom 7 (CB). Somehow, I think I know where is the
problem since GPRESSURE in energy output is really high while **PRESSURE is
not. I know **GPRESSURE has something to do with Hydrogen, and both atom 5
and 7 have Hydrogen bond and I am using rigid bond for H. Here is energy
output
PRESSURE: 500 -6837.73 -1.68605 65.7687 -3.01476 -6863.58 60.0149 13.4313
87.7551 -7571.61
GPRESSURE: 500 -6767.67 9.31771 81.6069 -32.143 -6790.96 57.5848 15.5408
106.813 -7513.94
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
POTENTIAL TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 500 20791.7593 16518.8416 80.3129
37.9625 -763971.6307 48307.5924 0.0000
0.0000 0.0000 -678235.1620 0.0000 -678235.1620
-678235.1620 0.0000 -7090.9746 -7024.1899
2414412.0000 -7090.9746 -7024.1899
*
*based on NAMD-mailing list suggestion i tried following solution but no
luck:
*
*increasing margin or/and energy minimization time, checking for overlapped
atom s
*
*I really appreciate your help,
*
*Mehran
*
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