Hi David,
You're missing the last 7592 bytes of the file. The question is why this is
not being flushed to disk. Do people see this specific behavior - I.e. the
end of the restart file being written on Linux Os's other than Ubuntu?
All the best
Ross
> -----Original Message-----
> From: David Condon [mailto:dec986.gmail.com]
> Sent: Tuesday, April 10, 2012 11:59 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Could not read velocities from restart file
>
> Hi Aron,
>
> the good rst file looks like:
>
> 0.2649094 -0.0844054 0.1286095 0.5432906 -0.2507783 -
> 0.0405266
> 0.3149803 0.0175057 0.3673056 -0.1782371 0.2128560 -
> 0.1884006
> 0.2371759 -0.3057067 0.5952768 -0.2354916 -0.9410148 -
> 0.0438329
> -0.1159288 -0.5434164 0.0047462 -0.1315556 0.4991617
> 0.4990561
> 0.0211907 0.8615705 0.9348652 0.0235789 -0.0474127
> 0.3410161
> -0.4567690 -0.3400850 0.2949318 -0.4300670 0.2233142
> 0.8368965
> -0.0714831 0.0409602 -0.1256436 0.2461557 0.4929560
> 1.0578373
> 0.1681050 -0.8414658 0.0167940 0.1557208 0.4892122 -
> 0.1181744
> -0.1883092 -0.3844528 -0.5576498 0.4514073 0.8922748 -
> 0.4837416
> 35.4095673 35.4095673 35.4095673 109.4712190 109.4712190
> 109.4712190
>
> and this bad one (4.rst) looks like:
>
> -0.0081777 -0.4593477 -0.0313187 0.0662137 -0.2243723
> 0.0759823
> -0.6695894 0.7636265 0.6048110 0.1985666 -0.4804675
> 0.0244801
> -0.3532630 -0.0377391 0.0271259 -0.1361401 -1.0299790
> 0.2153224
> 0.1951599 0.4482496 0.3146665 0.2586283 -0.0169079 -
> 0.0427295
> 0.0330675 -0.0438502 -0.2393299 0.2528661 0.1129621
> 0.3183243
> -0.0396155 -0.1839538 -0.0473871 -0.4539827 -0.5628476 -
> 0.1202268
> -0.6310506 0.2109399 0.4612384 0.0762229 0.2612662
> 0.3154209
> -0.8445841 -0.1361930 0.9036816 0.5807950 -0.5465261
> 0.3683826
> 0.0661990 0.1313591 -0.0815423 0.2405941 0.4207141 -
> 0.0614615
> 0.3071491 0.6133529 -0.1018300 -0.2264057 0.0919355 -
> 0.1983635
>
> The numbers at the bottom row appear to be of the wrong magnitude (or
> the
> bottom row is just missing).
>
> and to Ross Walker, I am using Linux 2.6.32-40-generic on Ubuntu 10.04
> Lucid Lynx.
>
> Thanks much for your help everyone!
> -Dave
>
> On Tue, Apr 10, 2012 at 2:18 PM, Aron Broom <broomsday.gmail.com>
> wrote:
>
> > are the restart files in ASCII? Can you open them up and have a look
> in
> > order to see what is wrong? Hopefully none of your values have
> become
> > 'NaN'.
> >
> > ~Aron
> >
> > On Tue, Apr 10, 2012 at 2:16 PM, David Condon <dec986.gmail.com>
> wrote:
> >
> > > Hi Dr. Steinbrecher,
> > >
> > > thanks much for your prompt reply! For some bizarre reason, even
> on
> > short
> > > re-runs the error is reproduced.
> > >
> > > The restart runs are in sequence:
> > >
> > > -rw-r--r-- 1 dave dave 252901 2012-04-10 08:33 New/1.rst
> > > > -rw-r--r-- 1 dave dave 252901 2012-04-10 08:33 New/2.rst
> > > > -rw-r--r-- 1 dave dave 252901 2012-04-10 08:33 New/3.rst
> > > > -rw-r--r-- 1 dave dave 245309 2012-04-10 12:59 New/4.rst
> > > >
> > > It looks like I will just have to wait until the 4th MD run
> finishes.
> > >
> > > regards,
> > > -Dave
> > >
> > >
> > > On Tue, Apr 10, 2012 at 10:08 AM, <steinbrt.rci.rutgers.edu> wrote:
> > >
> > > > Hi,
> > > >
> > > > > restarted the computer to install some updates (first by
> killing the
> > > > pmemd
> > > > > process, which may not have been the proper way).
> > > >
> > > > I would agree that this is not the proper way and that one should
> split
> > > > long simulations into pieces and keep intermediate rst-files
> (check the
> > > > ntwr<0 option) so that precisely this does not happen, but
> anyways:
> > > >
> > > > > Upon restarting the simulation, I get the error at the bottom
> of the
> > > new
> > > > > output file:
> > > > >
> > > > > | ERROR: Could not read velocities from 4.rst
> > > > >>
> > > >
> > > > Check if your rst file contains the correct 3*N number of
> coordinates
> > and
> > > > 3*N velocities. If you were unlucky enough to kill the process
> right
> > when
> > > > it was halfway done with writing a rst file, you may have
> truncated and
> > > > thereby corrupted it.
> > > >
> > > > However all is not lost I guess:
> > > >
> > > > if your rst file contains enough coordinates (3*natom, so
> natom/2+3
> > > lines)
> > > > and only misses velocities, you could delete all velocity lines
> and
> > just
> > > > restart your system (ntx=1) at 300K. This introduces a little
> > disturbance
> > > > but that should rapidly equilibrate away (in few ps). You may
> have to
> > > rest
> > > > the box in xleap, as box coordinates are at the end of the rst-
> file.
> > > >
> > > > If your rst file is unusable, you could extract the last snapshot
> from
> > > the
> > > > mdcrd-file and convert it into a rst (via ptraj) and restart your
> > > > simulation from that point. crd-files have a lower accuracy than
> > > > rst-files, but again, this should equilibrate away very quickly,
> > compared
> > > > to a multinanosecond simulation.
> > > >
> > > > if ptraj cannot read your crd file either, you can (if you used
> ASCII
> > > > mdcrd format) parse through the mdcrd by yourself and see if you
> can
> > > > extract a useful snapshot as far advanced in your trajectory as
> > possible
> > > > and restart from there.
> > > >
> > > > Each of these solutions would introduce a small but in my opinion
> > > > acceptable inaccuracy into your system. That may be difficult to
> > explain
> > > > in a paper, but otherwise you should be ok.
> > > >
> > > > For materials and methods: ;-)
> > > >
> > > > "At 1448 ns simulation time, velocities were discarded and
> replaced by
> > a
> > > > Boltzmann velocity distribution at room temerature. This
> procedure was
> > > > conducted to ensure proper system equilibration and stability.
> > (innocent
> > > > whistling)"
> > > >
> > > > Regards,
> > > >
> > > > Thomas
> > > >
> > > > Dr. Thomas Steinbrecher
> > > > formerly at the
> > > > BioMaps Institute
> > > > Rutgers University
> > > > 610 Taylor Rd.
> > > > Piscataway, NJ 08854
> > > >
> > > > _______________________________________________
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> > > >
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> > >
> >
> >
> >
> > --
> > Aron Broom M.Sc
> > PhD Student
> > Department of Chemistry
> > University of Waterloo
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Apr 10 2012 - 13:30:05 PDT
