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
> > >
> > > _______________________________________________
> > > 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
> >
>
>
>
> --
> 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 10 2012 - 12:00:06 PDT
