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
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Received on Tue Apr 10 2012 - 11:30:04 PDT
