Dear Ying,
If you are running this simulation via a queuing system such as PBS it is
possible that the error message is being lost. I would try restarting your
simulation from the poitn where it stopped with 'identical' options in the
mdin file. Except irest=1 and ntx=5. In the restart I would try setting
ntpr=1 and ntwx=1 so you can see exactly how far it gets before it stops,
you can also watch the trajectory in detail to see if anything obvious is
going astray.
I would also run this restart simulation interactively on your own machine
so that you see any error messages (don't use a queing system). If you get
any more information please post it to the list and we will be able to
comment further.
All the best
Ross
/\
\/
|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
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> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of ying xiong
> Sent: Monday, February 27, 2006 00:30
> To: amber.scripps.edu
> Subject: AMBER: MD job stopped without any error information?
>
>
> 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
> yxiong99.163.com
> 2006-02-27
>
>
>
> --------------------------------------------------------------
> ---------
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Received on Sun Mar 05 2006 - 06:10:09 PST
