Dear Amber-users,
I'm trying simulations with high temperature (363K), but after 82ps, the
temperature suddenly increased, showing errors like below, and then system
stopped.
First, I ran the system from 0K to 363K with restraints for 20ps, and then
started MD without restraints in 363K. I used 1fs as a timestep, so timestep
was low enough. When I looked at sys info (shown below), density looks OK, but
temp suddenly increased after 72ps, and then system stopped at 78ps. When I
looked at trajectories visually, I could see that octahedron water box keep
bigger, but I think that this is normal visualization effect.
Could you tell me what the problem is here?
---------------------
check COM velocity, temp: 0.002199 0.01(Removed)
NSTEP = 1000 TIME(PS) = 21.000 TEMP(K) = 361.70 PRESS = -469.0
Etot = -150932.9296 EKtot = 37874.5625 EPtot = -188807.4920
BOND = 1068.7437 ANGLE = 3324.6216 DIHED = 1606.1163
1-4 NB = 851.9263 1-4 EEL = -10208.7738 VDWAALS = 17581.2373
EELEC = -203031.3634 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 16789.9847 VIRIAL = 22745.4858 VOLUME = 588140.1388
Density = 0.9154
Ewald error estimate: 0.9907E-06
------------------------------------------------------------------------------
check COM velocity, temp: 0.002745 0.01(Removed)
NSTEP = 52000 TIME(PS) = 72.000 TEMP(K) = 364.45 PRESS = -30.7
Etot = -154266.2338 EKtot = 38162.4954 EPtot = -192428.7292
BOND = 997.2928 ANGLE = 3347.3729 DIHED = 1672.9867
1-4 NB = 879.1251 1-4 EEL = -10380.6882 VDWAALS = 18194.8596
EELEC = -207139.6781 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 16929.4654 VIRIAL = 17294.2248 VOLUME = 549891.6263
Density = 0.9791
Ewald error estimate: 0.5944E-04
------------------------------------------------------------------------------
vlimit exceeded for step 52001 ; vmax = 31.68132558266050
vlimit exceeded for step 52002 ; vmax = 324.7710216032469
check COM velocity, temp: 0.003104 0.01(Removed)
NSTEP = 53000 TIME(PS) = 73.000 TEMP(K) = 405.40 PRESS = 262.9
Etot = -146449.1258 EKtot = 42451.1823 EPtot = -188900.3081
BOND = 1648.8754 ANGLE = 4298.5353 DIHED = 1797.7468
1-4 NB = 962.8631 1-4 EEL = -10173.3107 VDWAALS = 18676.4127
EELEC = -206111.4306 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 17531.3452 VIRIAL = 14403.7479 VOLUME = 551048.4861
Density = 0.9770
Ewald error estimate: 0.1505E-04
------------------------------------------------------------------------------
vlimit exceeded for step 53004 ; vmax = 29.38773825237311
vlimit exceeded for step 53005 ; vmax = 24.03504379129096
check COM velocity, temp: 0.000912 0.00(Removed)
NSTEP = 58000 TIME(PS) = 78.000 TEMP(K) = 522.73 PRESS = 526.3
Etot = -125819.8631 EKtot = 54736.8260 EPtot = -180556.6891
BOND = 5936.3327 ANGLE = 7728.9428 DIHED = 1852.1317
1-4 NB = 1158.7140 1-4 EEL = -10209.8571 VDWAALS = 18585.6963
EELEC = -205608.6496 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 17506.1892 VIRIAL = 11173.3844 VOLUME = 557275.9529
Density = 0.9661
Ewald error estimate: 0.4616E-04
------------------------------------------------------------------------------
vlimit exceeded for step 58000 ; vmax = 28.41153502344077
vlimit exceeded for step 58001 ; vmax = 27.43356608541275
Coordinate resetting cannot be accomplished,
deviation is too large
iter_cnt, my_bond_idx, i and j are : 3 1981 3289 3291
-----------------------------------
Thanks for your help in advance.
best,
Hwankyu.
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Received on Fri Jul 29 2005 - 22:53:01 PDT
