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 - 09:30:05 PDT
