AMBER Archive (2005)

Subject: AMBER: the restarting error

From: zhli_2000_at_126.com
Date: Mon Apr 25 2005 - 09:08:02 CDT


Hi,all,
   The whole minimization of the complex with waters was interrupted,
because the net transmission didn't work well. So the minimization can't
complete. The following is the part of out file:
  ..........
  check COM velocity, temp: 0.000000 0.00(Removed)

 NSTEP = 243000 TIME(PS) = 343.000 TEMP(K) = 298.07 PRESS = 74.2
 Etot = -135776.3955 EKtot = 34230.4686 EPtot = -170006.8641
 BOND = 1390.9959 ANGLE = 3840.7207 DIHED = 2831.0646
 1-4 NB = 1771.5752 1-4 EEL = 19298.0512 VDWAALS = 18423.3245
 EELEC = -217562.5961 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 14257.9496 VIRIAL = 13364.8005 VOLUME = 557721.5180
                                                Density = 1.0248
 Ewald error estimate: 0.4038E-04
 ---------------------------------------------------------------------------

---

NSTEP = 243500 TIME(PS) = 343.500 TEMP(K) = 299.46 PRESS = -25.6 Etot = -135772.9031 EKtot = 34390.5275 EPtot = -170163.4306 BOND = 1333.4578 ANGLE = 3779.1680 DIHED = 2811.4527 1-4 NB = 1778.6720 1-4 EEL = 19250.4781 VDWAALS = 18629.4244 EELEC = -217746.0836 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 14448.9849 VIRIAL = 14756.8950 VOLUME = 557481.1031 Density = 1.0253 Ewald error estimate: 0.2375E-04 --------------------------------------------------------------------------- ---

check COM velocity, temp: 0.000000 0.00(Removed)

NSTEP = 244000 TIME(PS) = 344.000 TEMP(K) = 299.42 PRESS = 9.6 Etot = -135758.2209 EKtot = 34385.2687 EPtot = -170143.4896 BOND = 1387.1727 ANGLE = 3755.3665 DIHED = 2835.6052 1-4 NB = 1766.1725 1-4 EEL = 19358.7201 VDWAALS = 18301.0670 EELEC = -217547.5935 EHBOND = 0.0000 RESTRAINT = 0.0000 EKCMT = 14512.6075 VIRIAL = 14397.3689 VOLUME = 558003.0154 Density = 1.0243 Ewald error estimate: 0.2324E-05 --------------------------------------------------------------------------- ---

Especially unfortunately, the restart file wasn't written when the job was teminated incorrectly. So I use the ptraj input/output commands to creat the restart file of the last frame. Then continue doing the MD minimization in the constant temprature with amber7. The input file is &cntrl nstlim=500000, dt=0.001, ntx=5, irest=1, ntpr=500, ntwr=500, ntwx=500, tempi=298.15, temp0=298.15, ntt=1, tautp=2.0, ntb=2, ntp=1, ntc=2, ntf=2, nrespa=1, cut = 10.0, &end

But the restart minimization can't work well. The error as the following:

--------------------------------------------------- APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION using 5000.0 points per unit in tabled values TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 20197851 | TOTAL SIZE OF NONBOND LIST = 20197851 vlimit exceeded for step 0 ; vmax = Infinity

Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large NITER, NIT, LL, I and J are : 0 0 103 182 183

Note: This is usually a symptom of some deeper problem with the energetics of the system.

What can I do to deal with this problem? Thank you for help in advance.

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