Hi Seren,
It definitely looks to me like you are running the serial version of sander
but with mpirun. Make sure you are using a parallel version of the code.
Make sure the executable given to mpirun is sander.MPI and NOT just sander.
All the best
Ross
> -----Original Message-----
> From: Seren Soner [mailto:seren.soner.gmail.com]
> Sent: Friday, October 29, 2010 9:10 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Output problem on Amber 9
>
> Thanks for the reply Adrian.
>
> But I'm afraid that isnt the case. In fact, I just reinstalled AMBER on a
> clean and fresh server using MPICH2.
>
> The tests all seem just fine, and the run keeps going, but the coordinate
> file is corrupt (according to ptraj), and the .out file from the pmemd is
as
> following:
>
> NSTEP = 5005 TIME(PS) = 10.010 TEMP(K) = 293
> NSTEP = 5020 TIME(PS) = 10.040 TEMP(K) = 292.63 PRESS =
> 274.9
> Etot = -206080.1422 EKtot = 50018.8412 EPtot =
> -256098.9834
> BOND = 1158.7574 ANGLE = 3226.4692 DIHED =
> 4959.5549
> 1-4 NB = 1696.6991 1-4 EEL = 21230.7542 VDWAALS =
> 32958.6284
> EELEC = -321329.8466 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 22722.9567 VIRIAL = 17729.8009 VOLUME =
> 841143.0522
> Density =
> 1.0138
> Ewald error estimate: 0.5244E-04
> --------------------
> NSTEP = 5010 TIME(PS) = 10.020 TEMP(K) = 293
> NSTEP = 5025 TIME(PS) = 10.050 TEMP(K) = 293.83 PRESS =
> 220.5
> Etot = -206067.1820 EKtot = 50223.4622 EPtot =
> -256290.6442
> BOND = 1143.5592 ANGLE = 3270.5782 DIHED =
> 4942.4778
> 1-4 NB = 1674.3206 1-4 EEL = 21252.6748 VDWAALS =
> 32893.7176
> EELEC = -321467.9724 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 22820.5212 VIRIAL = 18815.7936 VOLUME =
> 841238.7879
> Density =
> 1.0137
> Ewald error estimate: 0.4236E-04
> --------------------
> NSTEP = 5015 TIME(PS) = 10.030 TEMP(K) = 292
> NSTEP = 5030 TIME(PS) = 10.060 TEMP(K) = 293.63 PRESS =
> 162.4
> Etot = -206054.1128 EKtot = 50189.3052 EPtot =
> -256243.4180
> BOND = 1095.1010 ANGLE = 3234.5279 DIHED =
> 4948.3120
> 1-4 NB = 1664.1808 1-4 EEL = 21271.6600 VDWAALS =
> 32890.3861
> EELEC = -321347.5860 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 22884.4044 VIRIAL = 19934.3426 VOLUME =
> 841311.4130
> Density =
> 1.0136
> Ewald error estimate: 0.6402E-04
> --------------------
> NSTEP = 5020 TIME(PS) = 10.040 TEMP(K) = 292
> NSTEP = 5035 TIME(PS) = 10.070 TEMP(K) = 292.97 PRESS =
> 108.3
> Etot = -206041.0229 EKtot = 50075.8387 EPtot =
> -256116.8616
> BOND = 1188.6496 ANGLE = 3253.7780 DIHED =
> 4958.3474
> 1-4 NB = 1657.4676 1-4 EEL = 21231.7085 VDWAALS =
> 32913.2619
> EELEC = -321320.0746 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 22908.5928 VIRIAL = 20940.4972 VOLUME =
> 841363.6741
> Density =
> 1.0136
> Ewald error estimate: 0.9973E-04
> --------------------
>
>
> There seems to be a problem of synchronization, but I don't have any idea
> what causes it, or what can solve it.
>
> Thanks,
> Seren Soner
>
> On Mon, Oct 18, 2010 at 1:40 PM, Adrian Roitberg
> <roitberg.qtp.ufl.edu>wrote:
>
> > I have seen this before, and it is usually due to more than one instance
> > of amber trying to write to the same files. Check that there is only one
> > set of amber runs active in that directory.
> >
> > Adrian
> >
> >
> > On 10/18/10 11:16 AM, Seren Soner wrote:
> > > Hello there,
> > >
> > > I've been using AMBER in our server for some time, and after the
> > > server crash a few weeks back, my output files have been acting weird.
> > > My computer administrator tells me nothing has been changed after the
> > > server crash, and the output file becomes as follows:
> > >
> > >
> > > NSTEP = 219965 TIME(PS) = 12939.930 TEMP(K) = 299
> > > NSTEP = 220080 TIME(PS) = 12940.160 TEMP(K) = 299.63 PRESS = 79.6
> > > Etot = -203606.8511 EKtot = 51214.7469 EPtot = -254821.5980
> > > BOND = 1362.7033 ANGLE = 3547.3148 DIHED = 4862.2996
> > > 1-4 NB = 1683.6634 1-4 EEL = 21484.6416 VDWAALS = 32232.8437
> > > EELEC = -319995.0644 EHBOND = 0.0000 RESTRAINT = 0.0000
> > > EKCMT = 23099.5614 VIRIAL = 21648.8530 VOLUME = 844163.5532
> > >
> > > Or, sometimes I may see NSTEP = 219000 information at one line, and
> > > then NSTEP = 218990, NSTEP = 218995, and NSTEP = 219000 again.
> > >
> > > Does anyone have any idea what may cause this problem ?
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> > --
> > Dr. Adrian E. Roitberg
> > Associate Professor
> > Quantum Theory Project, Department of Chemistry
> > University of Florida
> >
> > Senior Editor. Journal of Physical Chemistry.
> >
> > on Sabbatical in Barcelona until August 2011.
> > Email roitberg.ufl.edu
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Fri Oct 29 2010 - 09:30:06 PDT
