Dear Ambers,
I'm running a conventional MD simulation on a protein with phosphorylated residue, using sander.MPI in AMBER9. When I was minimizing the solvated structure, the simulation underwent an unusual increase in 1-4 ELE, and then core dumped. I wonder how this could take place, and how I could solve the problem. Thanks!
NSTEP ENERGY RMS GMAX NAME NUMBER
60 -1.4056E+05 1.3113E+01 2.9107E+03 H1P 2919
BOND = 9103.6824 ANGLE = 694.3305 DIHED = 2952.2351
VDWAALS = 16629.9368 EEL = -182200.1707 HBOND = 0.0000
1-4 VDW = 1096.0739 1-4 EEL = 11142.6092 RESTRAINT = 18.7001
EAMBER = -140581.3028
NSTEP ENERGY RMS GMAX NAME NUMBER
80 -1.9038E+05 1.1071E+05 2.3945E+07 O2P 2917
BOND = 9090.0938 ANGLE = 688.5494 DIHED = 2952.2264
VDWAALS = 16630.2145 EEL = -182201.1899 HBOND = 0.0000
1-4 VDW = 1096.0431 1-4 EEL = -38651.2584 RESTRAINT = 18.5844
EAMBER = -190395.3212
NSTEP ENERGY RMS GMAX NAME NUMBER
100 -1.1732E+06 4.6658E+07 1.0092E+10 O2P 2917
BOND = 9090.1720 ANGLE = 688.6065 DIHED = 2952.2263
VDWAALS = 16630.2146 EEL = -182201.1877 HBOND = 0.0000
1-4 VDW = 1096.0431 1-4 EEL = -1021515.1740 RESTRAINT = 18.5857
EAMBER = -1173259.0993
NSTEP ENERGY RMS GMAX NAME NUMBER
120 -9.5927E+07 4.0103E+11 8.6740E+13 H1P 2919
BOND = 9090.1760 ANGLE = 688.6095 DIHED = 2952.2263
VDWAALS = 16630.2146 EEL = -182201.1876 HBOND = 0.0000
1-4 VDW = 1096.0431 1-4 EEL = ************* RESTRAINT = 18.5857
EAMBER = *************
--------------
zgleo
2007-06-21
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Received on Sun Jun 24 2007 - 06:07:19 PDT
