Re: [AMBER] Regarding problem with self guided molecular dynamics

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 23 Mar 2010 13:21:11 -0400

Hello,

Perhaps you submitted it to a queue and you ran out of wall-time? Do
the tests pass? (in both serial and parallel) Maybe your files are
getting too large and amber can no longer handle it? You are printing
out very frequently... It's unlikely that anyone will try and
reproduce your error since it doesn't occur until the 283,000th step
or so.

Perhaps try reducing output frequency (ntwx=1000, ntpr=1000) and see
if that helps at all? (How large are your files?)

Good luck!
Jason

On Tue, Mar 23, 2010 at 2:02 AM, aneesh cna <aneeshcna.gmail.com> wrote:
> Dear amber users,
>
>                    I am doing SGMD (self guided molecular dynamics) with
> Amber 9.0 version. But the simulation get terminated with some error as
> shown below after 6ns run.
>
> ******************************************************************************************
> MPI Application rank 11 exited before MPI_Finalize() with status 1
> forrtl: error (78): process killed (SIGTERM)
> Image              PC                Routine            Line
> Source
> libpthread.so.0    0000003CE890C4F0  Unknown               Unknown  Unknown
> libmpi.so.1        0000002A956EBDDD  Unknown               Unknown  Unknown
> libmpi.so.1        0000002A956D7165  Unknown               Unknown  Unknown
> libmpi.so.1        0000002A957437DA  Unknown               Unknown  Unknown
> libmpi.so.1        0000002A95733C88  Unknown               Unknown  Unknown
> libmpi.so.1        0000002A95749F20  Unknown               Unknown  Unknown
> sander.MPI         00000000004ED9AF  Unknown               Unknown  Unknown
> sander.MPI         00000000004BD5D4  Unknown               Unknown  Unknown
> sander.MPI         00000000004B2FAD  Unknown               Unknown  Unknown
> sander.MPI         0000000000404DA2  Unknown               Unknown  Unknown
> libc.so.6          0000003CE821C3FB  Unknown               Unknown  Unknown
> sander.MPI         0000000000404CEA  Unknown               Unknown  Unknown
> forrtl: error (78): process killed (SIGTERM)
> **********************************************************************************************
>
> Here is input for SGMD.........
>
>
> ********************************************************
>  &cntrl
>  imin = 0, ntx = 7, irest = 1,
>  ntpr = 100, ntwx = 500, ntwe = 0,
>  ntc = 2, ntf = 2,iwrap = 0,
>  nstlim = 1000000, dt =0.002,
>  tempi=274.0, temp0 = 274.0, ntt =1, tautp =1.0,
>  ntb = 1, ntp = 0,cut =12.0,
>  isgld =1, tsgavg =0.2, tempsg =1.0,
>  isgsta =8701, isgend =8826    ( atom numbers of protein)
>  &end
> **********************************************************
>
>
> and at the end of the run the output file look like as
> shown.................
>
> ***************************************************************************************************
> NSTEP =   233800   TIME(PS) =    6767.600  TEMP(K) =   289.61  PRESS =
> 0.0
>  Etot   =    -11218.2624  EKtot   =      7343.7475  EPtot      =
> -18562.0099
>  BOND   =      2779.1812  ANGLE   =      3562.7218  DIHED      =
> 4418.6891
>  1-4 NB =      1301.6957  1-4 EEL =     26368.3968  VDWAALS    =
> -4423.1948
>  EELEC  =    -52569.4997  EHBOND  =         0.0000  RESTRAINT  =
> 0.0000
>  Ewald error estimate:   0.1366E-04
> SGFT=    0.8172      TEMPSGI=    1.0000 K
>  ------------------------------------------------------------------------------
>
>
>  NSTEP =   233900   TIME(PS) =    6767.800  TEMP(K) =   284.05  PRESS =
> 0.0
>  Etot   =    -11117.5166  EKtot   =      7202.8946  EPtot      =
> -18320.4112
>  BOND   =      2829.0841  ANGLE   =      3809.7204  DIHED      =
> 4370.6374
>  1-4 NB =      1333.1363  1-4 EEL =     26341.0330  VDWAALS    =
> -4377.1936
>  EELEC  =    -52626.8286  EHBOND  =         0.0000  RESTRAINT  =
> 0.0000
>  Ewald error estimate:   0.5218E-04
> SGFT=    0.6368      TEMPSGI=    1.0000 K
>  ------------------------------------------------------------------------------
> *************************************************************************************************************
>
> what could be the reason for this early termination? Waiting for your
> valuable reply....
>
>
>
> Thanks in advance
>
> Sincerely
> Aneesh
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Mar 23 2010 - 10:30:04 PDT
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