From: Aron Broom (broomsday_at_gmail.com)
Date: Fri Jun 15 2012 - 21:24:20 CDT
well, there are two separate options:
binaryoutput
and
binaryrestart
but I can't imagine you would have "binaryrestart yes" without knowing it,
so it is rather puzzling.
On Fri, Jun 15, 2012 at 9:25 PM, <amin_at_imtech.res.in> wrote:
> Thanks. I already know my files are binary.My other questions were that
> why my
> restart files are binary when I have binary output off in my configuration
> file.And secondly why my final output coor and vel files are not binary
> while
> restart files are binary?
>
>
> > I am slightly confused by what you have written, but I think there are a
> > few points on which I can comment:
> >
> > 1) when you load binary coordinates and velocities, you need to supply a
> > PDB file as you say. But, that PDB file itself is NOT ignored, it is
> > simply that the coordinates from that file are not used. If the whole
> file
> > was ignored it wouldn't be needed. I'm not sure, but I believe it is
> > needed in order to assign the atoms and such, but then the actual values
> of
> > the x,y,z coordinates from the binary file are used.
> >
> > 2) You can easily check if your files are binary or not by opening them
> in
> > something like gedit, vim, or nano. If they are not binary, they should
> be
> > human readable, much like a PDB file. If they are binary they will not
> > be. In a lot of linux distros the thumbnail for a binary file will
> clearly
> > have 0's and 1's on it, rather than a preview of the text.
> >
> > 3) if you loaded the file as a bincoordinates, and the simulation
> actually
> > ran without giving all kinds of crazy velocity or constraint errors,
> than I
> > suspect it is fine. If the coordinates were totally messed up, you
> > wouldn't be able to just restart.
> >
> > 4) if you want to be really certain, load the questionable coordinates in
> > VMD. If it is ASCII, you will be able to load just the coordinates file
> on
> > it's own as PDB type, if it is binary, you'll need to load the PSF first
> > and the coordinates will then be loaded as NAMD or something like that.
> >
> > ~Aron
> >
> > On Fri, Jun 15, 2012 at 8:43 PM, <amin_at_imtech.res.in> wrote:
> >
> >> Dear all,
> >> I am trying to restart my simulation from the restart coor and vel
> >> files.
> >> However I keep getting an error like "FATAL ERROR : Line too long in pdb
> >> file". I checked the archives and found that this may be because the
> coor
> >> file is binary and I may have to add a line bincoordinates and do the
> same
> >> for velocities. I did this and I was able to restart the simulation.
> >> However, I have a few doubts:
> >> 1) Why is a binary restart coor file being written when I have mentioned
> >> "binary
> >> output off" in my configuration file?
> >> 2)When a simulation run is finished, and the last coor and vel files are
> >> generated, then I am able to restart the simulation with coordinates and
> >> velocities (not bin). However I need to have bincoordinates to restart
> >> simulations from coor and vel files generated at various steps during
> the
> >> run.
> >> 3)I learnt from the manual that even when using bincoordinates, I need
> to
> >> have
> >> coordinates line in the configuration file however it will be ignored.
> >> Therefore, I tried to restart the simulation with some random name in
> the
> >> coordinates line but it complains of not finding the pdb file and works
> >> only
> >> when I mention the real file name (ionized.pdb)in the coordinates
> >> line.Does that
> >> mean that the original PDB and PSF files are being used to restart and
> not
> >> the
> >> restart.coor file?
> >>
> >> Any help will be appreciated.
> >>
> >> Amin.
> >>
> >> ______________________________________________________________________
> >> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
> >> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
> >> सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
> >> पिन कोड/PIN CODE :160036
> >> दूरभाष/EPABX :0172 6665 201-202
> >>
> >>
> >
> >
> > --
> > Aron Broom M.Sc
> > PhD Student
> > Department of Chemistry
> > University of Waterloo
> >
>
>
>
> ______________________________________________________________________
> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
> सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
> पिन कोड/PIN CODE :160036
> दूरभाष/EPABX :0172 6665 201-202
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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