AMBER Archive (2006)

Subject: Re: AMBER: MD job stopped without any error information?

From: Melinda Layten (mlayten_at_gmail.com)
Date: Mon Feb 27 2006 - 09:18:09 CST

Just a guess, but do you have iwrap=1. Otherwise the default is iwrap=0 and
water molecules can drift too far to continue a simulation. (Do a search of
the mailing list on iwrap, this happens a lot)

Melinda Layten

On 2/27/06, ying xiong <yxiong99_at_163.com> wrote:
>
>
> Dear sir,
> When I run a MD job in which all the backbone atoms were fixed, the
> job stopped without any error information. Please see the last step:
>
> ------------------------------------------------------------------------------
> check COM velocity, temp: 0.001876 0.01(Removed)
>
> NSTEP = 66000 TIME(PS) = 132.000 TEMP(K) = 297.26 PRESS = 0.0
> Etot = -115497.8257 EKtot = 26774.9162 EPtot = -142272.7419
> BOND = 734.6621 ANGLE = 2500.8806 DIHED = 3090.1269
> 1-4 NB = 1467.5182 1-4 EEL = 13090.5211 VDWAALS = 10526.5964
> EELEC = -174608.9002 EHBOND = 0.0000 RESTRAINT = 925.8531
> EAMBER (non-restraint) = -143198.5950
> Ewald error estimate: 0.4388E-04
>
> ------------------------------------------------------------------------------
> When I restart this job, it still can't continue. Please see the
> information:
> What's matter with this job?
>
> -------------------------------------------------------------------------------
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
> ---------------------------------------------------
> 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 = 4750811
> | TOTAL SIZE OF NONBOND LIST = 15671042
>
> NSTEP = 0 TIME(PS) = 132.000 TEMP(K) = 436.06 PRESS = -600.3
> Etot = -102985.4337 EKtot = 39276.1242 EPtot = -142261.5579
> BOND = 759.6675 ANGLE = 2531.1736 DIHED = 3092.8915
> 1-4 NB = 1466.2119 1-4 EEL = 13072.9271 VDWAALS = 10548.0487
> EELEC = -174625.7221 EHBOND = 0.0000 RESTRAINT = 893.2438
> EAMBER (non-restraint) = -143154.8017
> EKCMT = 11578.5782 VIRIAL = 18515.4088 VOLUME = 535195.5139
> Density = 0.8374
> Ewald error estimate: 0.9154E-04
>
> ------------------------------------------------------------------------------
>
>
>
> ying xiong
> yxiong99_at_163.com
> 2006-02-27
>
>
>
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