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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