From: amin_at_imtech.res.in
Date: Fri Jun 15 2012 - 20:25:57 CDT
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
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