From: 辛志宏 (xzhfood_at_njau.edu.cn)
Date: Wed Sep 09 2020 - 23:03:53 CDT
Dear all,
I am running a QM/MM in a minimization simulation and come across an error as follows, I searched the namd mailing list and re-setup the "cellOrigin" parameter by PBC box, however, the issue still not solved, how to fix the issue? Any suggestion will be much appreciated.
the constrain parameter
# mobile atom selection:
constraints on
consexp 2
consref YZZ-restraint.pdb
conskfile YZZ-restraint.pdb
conskcol B
constraintScaling 2.0 #(when the value set to 5, an error will occured )
the minization parameter
# Number of steps in the QM/MM simulation.
minimize 100
run 2000
the error information,
............................
ERROR: Atom 1450 velocity is 44316.2 -3353.86 6839.1 (limit is 24000, atom 353 of 1140 on patch 12 pe 2)
ERROR: Atom 1452 velocity is -45752.6 3605.38 -6493.9 (limit is 24000, atom 355 of 1140 on patch 12 pe 2)
ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on patch 12 pe 2).
WRITING COORDINATES TO DCD FILE YZZ-QM-min-out.dcd AT STEP 106
PRESSURE: 106 3.31643e+07 -558377 1.32687e+06 -1.12782e+06 3.0385e+07 -219407 567553 -178116 2.87595e+07
GPRESSURE: 106 2.94489e+07 -265347 697993 -825602 3.01241e+07 -211842 63017.7 -129475 2.83545e+07
TIMING: 106 CPU: 39.6919, 0.710148/step Wall: 43196, 1051.59/step, 582.464 hours remaining, 1200.250000 MB of memory in use.
ENERGY: 106 312845.5932 85634.6330 2984.7089 556.0897 -117499.8095 11452066.5021 23532359.8716 -2151894.5182 6038397.7682 39155450.8389 68833.6161 33117053.0707 37421208.5062 68833.6161 30769621.5966 29309160.5714 91937.0412 30769621.5966 29309160.5714
FATAL ERROR: Exiting prematurely; see error messages above.
Zhi hong Xin
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