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
..................................
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jan 14 2004 - 15:53:15 PST
