AMBER Archive (2007)

Subject: AMBER: sander core dumped during minimization

From: zgleo (zgleo_at_tom.com)
Date: Wed Jun 20 2007 - 20:51:04 CDT

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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