AMBER Archive (2005)

Subject: Re: AMBER: the restarting error

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Mon Apr 25 2005 - 09:37:50 CDT

Hi,

You should try to do the minimization with no SHAKE. And what do you
mean by "net transmission"? The input file you gave looks to me a MD
input. MD and minimization are two different options set by imin flag.
The default is imin=0, which is MD. I suggest you take a look at AMBER
tutorial page for examples of running sander or perhaps the book by
Andrew Leach "Molecular Modeling:...".

Good luck.

Guanglei

zhli_2000_at_126.com wrote:
>
> 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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