AMBER: strange output of MD

From: L Jin <s0344557.sms.ed.ac.uk>
Date: Wed, 7 Jan 2004 16:42:49 +0000

Hi,

I have just built up a small molecule. And I ran the Minimization first and then
MD as usual. All the input files and options were good for previeous simulation
but this time the MD output is strange while the minimization is good I think.
Would you please help me to find what is wrong with this? Any suggestion is
welcome. Thanks in advance.

min.in :

 minimization with sander (Amber7)
 &cntrl
  imin = 1, maxcyc = 50000, drms = 0.0005, ntb = 0,
  ntpr = 1000, cut = 999., ncyc = 100,
 &end

minimizaiton result :

 4. RESULTS
--------------------------------------------------------------------------------

 ---------------------------------------------------

     eedmeth=4: Setting switch to one everywhere

 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 303
| TOTAL SIZE OF NONBOND LIST = 303


   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 2.3391E+04 3.2374E+04 2.0326E+05 O30 11

 BOND = 0.0023 ANGLE = 12.3206 DIHED = 4.3342
 VDWAALS = 23565.9892 EEL = -289.6052 HBOND = 0.0000
 1-4 VDW = 9.2099 1-4 EEL = 88.7886 RESTRAINT = 0.0000


                    FINAL RESULTS



   NSTEP ENERGY RMS GMAX NAME NUMBER
    622 -1.2307E+02 4.4446E-04 1.6950E-03 OS3 30

 BOND = 4.4854 ANGLE = 27.1946 DIHED = 9.3549
 VDWAALS = 2.6568 EEL = -227.1559 HBOND = 0.0000
 1-4 VDW = 6.4332 1-4 EEL = 53.9580 RESTRAINT = 0.0000





md.in :

MD in-vacuo, 999.0 angstrom cutoff
 &cntrl
   igb = 0, ntb = 0, ntpr = 100, ntwx = 100, ntwe = 100,

   cut = 999.0, ntc = 2, ntf = 2,

   tempi = 300.0, temp0 = 300.0, ntt = 1, tautp = 0.5,

   imin = 0,
   nstlim = 1000000, dt = 0.001,

 &end


MD result :

 4. RESULTS
--------------------------------------------------------------------------------

 ---------------------------------------------------

     eedmeth=4: Setting switch to one everywhere

 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 303
| TOTAL SIZE OF NONBOND LIST = 303

 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 512.36 PRESS = 0.0
 Etot = 23429.7296 EKtot = 38.6900 EPtot = 23391.0395
 BOND = 0.0023 ANGLE = 12.3206 DIHED = 4.3342
 1-4 NB = 9.2099 1-4 EEL = 88.7886 VDWAALS = 23565.9892
 EELEC = -289.6052 EHBOND = 0.0000 RESTRAINT = 0.0000
 ------------------------------------------------------------------------------

 vlimit exceeded for step 0; vmax = 239.74953
 vlimit exceeded for step 1; vmax = 23.5008907
 vlimit exceeded for step 2; vmax = 26.1393824
 vlimit exceeded for step 3; vmax = 25.5655423
 vlimit exceeded for step 4; vmax = 23.6688948
 vlimit exceeded for step 5; vmax = 22.8694507
 vlimit exceeded for step 6; vmax = 22.4840646
 vlimit exceeded for step 7; vmax = 22.0533289
 vlimit exceeded for step 8; vmax = 21.4179993
 vlimit exceeded for step 9; vmax = 20.4642249
 vlimit exceeded for step 11; vmax = 22.7483904
 vlimit exceeded for step 12; vmax = 20.5535493
 vlimit exceeded for step 14; vmax = 22.3804833
 vlimit exceeded for step 15; vmax = 23.5173074
 vlimit exceeded for step 16; vmax = 22.4358259
 vlimit exceeded for step 17; vmax = 21.0062408
 vlimit exceeded for step 18; vmax = 21.2538154
 vlimit exceeded for step 19; vmax = 23.4737768
 vlimit exceeded for step 20; vmax = 20.8553961
 vlimit exceeded for step 24; vmax = 20.4809204
 vlimit exceeded for step 25; vmax = 23.4410997
 vlimit exceeded for step 26; vmax = 20.7577739
 vlimit exceeded for step 46; vmax = 27.8363363
 vlimit exceeded for step 47; vmax = 24.3060465
 vlimit exceeded for step 49; vmax = 20.466893
 vlimit exceeded for step 50; vmax = 20.4362349
 vlimit exceeded for step 56; vmax = 21.160895
 vlimit exceeded for step 61; vmax = 23.7883845
 vlimit exceeded for step 62; vmax = 21.954278
 vlimit exceeded for step 65; vmax = 22.5892485
 vlimit exceeded for step 66; vmax = 22.5105939
 vlimit exceeded for step 67; vmax = 89.2320946
 vlimit exceeded for step 68; vmax = 32.9823547
 vlimit exceeded for step 69; vmax = 24.9830047
 vlimit exceeded for step 70; vmax = 20.1649392
 vlimit exceeded for step 72; vmax = 407.045779
 vlimit exceeded for step 73; vmax = 24.2828465
 vlimit exceeded for step 74; vmax = 33.0379727
 vlimit exceeded for step 75; vmax = 25.9092008
 vlimit exceeded for step 76; vmax = 95.2343432
 vlimit exceeded for step 77; vmax = 22.3993751
 vlimit exceeded for step 78; vmax = 25.9145167
 vlimit exceeded for step 80; vmax = 23.2129516
 vlimit exceeded for step 81; vmax = 20.6378526
 vlimit exceeded for step 82; vmax = 20.7739306
 vlimit exceeded for step 83; vmax = 21.5326213
 vlimit exceeded for step 86; vmax = 23.4757537
 vlimit exceeded for step 87; vmax = 25.159433
 vlimit exceeded for step 88; vmax = 24.7407928
 vlimit exceeded for step 89; vmax = 23.3026743
 vlimit exceeded for step 90; vmax = 74.2743003
 vlimit exceeded for step 92; vmax = 26.4045923
 vlimit exceeded for step 93; vmax = 33.6475196
 vlimit exceeded for step 94; vmax = 24.4433618
 vlimit exceeded for step 95; vmax = 24.4678468
 vlimit exceeded for step 97; vmax = 21.8722025
 vlimit exceeded for step 98; vmax = 24.3063027
 vlimit exceeded for step 99; vmax = 24.2051252

 NSTEP = 100 TIME(PS) = 0.100 TEMP(K) =124258.88 PRESS = 0.0

 Etot = 14558.2503 EKtot = 9383.1962 EPtot = 5175.0542
 BOND = 3658.3823 ANGLE = 1128.2936 DIHED = 15.3211
 1-4 NB = 379.5951 1-4 EEL = 137.9489 VDWAALS = 44.2845
 EELEC = -188.7713 EHBOND = 0.0000 RESTRAINT = 0.0000
 ------------------------------------------------------------------------------

 vlimit exceeded for step 100; vmax = 23.7243971
 vlimit exceeded for step 101; vmax = 20.6473859
 vlimit exceeded for step 112; vmax = 21.692854
 vlimit exceeded for step 113; vmax = 21.9193763
 vlimit exceeded for step 114; vmax = 20.7675781
 vlimit exceeded for step 115; vmax = 23.2527799

..................................


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Received on Wed Jan 14 2004 - 15:53:15 PST
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