Re: [AMBER] Could not read velocities from restart file

From: Ross Walker <ross.rosswalker.co.uk>
Date: Tue, 10 Apr 2012 15:49:33 -0700

Hi David,

Assuming a fully up to date AMBER 11 could you try the attached patch
please.

Do a make clean and then save the file in $AMBERHOME/src/pmemd/src

cd $AMBERHOME/src/pmemd/src
patch -p0 <2012_04_10_restrt_patch.dat

Then do a recompile of pmemd, pmemd.MPI and pmemd.cuda and let me know if
the problem goes away.

All the best
Ross

> -----Original Message-----
> From: Ross Walker [mailto:ross.rosswalker.co.uk]
> Sent: Tuesday, April 10, 2012 3:32 PM
> To: 'AMBER Mailing List'
> Subject: Re: [AMBER] Could not read velocities from restart file
>
> Hi David,
>
> Are you using AMBER 11 or AMBER 12?
>
> 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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> > > >
> > >
> > >
> > >
> > > --
> > > Aron Broom M.Sc
> > > PhD Student
> > > Department of Chemistry
> > > University of Waterloo
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> > >
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Received on Tue Apr 10 2012 - 16:00:06 PDT
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