As Dan said, we can't help much with no error message. Try pmemd instead of
sander, it is less susceptible to this kind of behavior (and try running in
serial before you run in parallel to make sure it isn't an MPI-related
problem).
HTH,
Jason
On Wed, Aug 3, 2011 at 2:02 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Unfortunately since there is no error message it's difficult to
> determine what might be going wrong here; it could be sander, or it
> could be something with your system. Were you able to successfully run
> the test cases?
>
> -Dan
>
> On Wed, Aug 3, 2011 at 4:51 AM, tien dung <ttdung1100.yahoo.com> wrote:
> >
> >
> >
> >
> >
> > Hi all amber users,
> > I am very new in amber. MD production stop at prod47.out. It is not
> written any thing.
> > This is the content of prof47.out :
> >
> >
> > -------------------------------------------------------
> > Amber 11 SANDER 2010
> > -------------------------------------------------------
> >
> > | Run on 08/01/2011 at 09:06:06
> > [-O]verwriting output
> >
> > File Assignments:
> > | MDIN:
> > prod.in
> > | MDOUT: prod47.out
> > |INPCRD:
> > prod46.rst
> > | PARM: topol/complex.prmtop
> > |RESTRT:
> > prod47.rst
> > | REFC: refc
> > | MDVEL:
> > mdvel
> > | MDEN: mden
> > | MDCRD:
> > prod47.mdcrd
> > |MDINFO: mdinfo
> > | MTMD:
> > mtmd
> > |INPDIP: inpdip
> > |RSTDIP:
> > rstdip
> >
> > |INPTRA: inptraj
> > |
> >
> > Here is the input file:
> >
> > prod
> > ras-raf
> > &cntrl
> >
> > imin=0,irest=1,ntx=5,
> > nstlim=250000,dt=0.002,
> >
> > ntc=2,ntf=2,
> > cut=12.0, ntb=2, ntp=1, taup=2.0,
> > ntpr=5000,
> > ntwx=5000,
> > ntt=3, gamma_ln=2.0,
> >
> > ig=-1,
> > temp0=300.0,
> > /
> >
> >
> --------------------------------------------------------------------------------
> > 1. RESOURCE USE:
> >
> --------------------------------------------------------------------------------
> >
> > | Flags:
> > MPI
> > getting new box info from bottom of inpcrd
> > | INFO: Old style inpcrd file read
> >
> >
> >
> >
> >
> > It do not have any initial value. And there are not have prmtop and rst
> file for prod47. Job on cluster still run. But it is not writen anything in
> prod47.out .Can any one explain that ? I need to run more from prod47 to
> prod80.
> >
> > I am really appreciate. Thanks a lot
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Aug 03 2011 - 11:30:03 PDT
