From: Aron Broom (broomsday_at_gmail.com)
Date: Sat Jun 16 2012 - 21:22:29 CDT
I doubt that apoa1.pdb file is in binary, it is probably ASCII.
When you say "binaryoutput yes" you just mean that you want the
apoa1-out.coor file to be in binary rather than ASCII, but it doesn't
affect what you supply as the input for that run.
So, if you only have a PDB file for input, you should say "binaryoutput
yes", but then just have "coordinates apoa1.pdb". If you later want to use
the output from that run, then you will provide the new coordinates as:
"coordinates apoa1.pdb"
"bincoordinates apoa1-out.coor"
In this way the binary coordinates are used, but the ASCII coordinate file
is still required to assign the atoms or something of that sort, even
though the positions are ignored.
~Aron
On Sat, Jun 16, 2012 at 8:33 PM, Carlos Sosa <sosa0006_at_r.umn.edu> wrote:
> Aaron,
>
> I used this option but when I run the mem optimized version I get this
> error... Also, I did not see any difference in the apoa1.pdb file before
> and after generating the compressed psf file.
>
> Info: Running with 1 output processors (1 of them will output
> simultaneously).
> FATAL ERROR: Incorrect atom count in binary file ./apoa1.pdb
> CmiAbort is calling on PE:0
> aborting job:
> FATAL ERROR: Incorrect atom count in binary file ./apoa1.pdb
>
> configuration file:
> cellBasisVector1 108.8612 0.0 0.0
> cellBasisVector2 0.0 108.8612 0.0
> cellBasisVector3 0.0 0.0 77.758
> cellOrigin 0.0 0.0 0.0
>
> bincoordinates apoa1.pdb
> temperature 300
> seed 74269
>
> useCompressedPsf on
> switching on
> switchdist 10
> cutoff 12
> pairlistdist 13.5
> margin 0
> stepspercycle 20
>
> PME on
> PMEGridSizeX 108
> PMEGridSizeY 108
> PMEGridSizeZ 80
>
> structure apoa1.psf.inter
> parameters par_all22_prot_lipid.xplor
> parameters par_all22_popc.xplor
> exclude scaled1-4
> 1-4scaling 1.0
>
> timestep 1.0
> fullElectFrequency 4
>
> numsteps 500
> outputtiming 20
>
> outputname ./apoa1-out
>
>
>
> On Fri, Jun 15, 2012 at 4:18 PM, Aron Broom <broomsday_at_gmail.com> wrote:
>
>> when you do a run, have:
>>
>> binaryoutput yes
>>
>> in the config file.
>>
>> Then your coor, vel, and dcd files will be binary.
>>
>>
>> On Fri, Jun 15, 2012 at 4:43 PM, Carlos Sosa <sosa0006_at_r.umn.edu> wrote:
>>
>>>
>>> Hello,
>>>
>>> Any information on how to obtain binary format representation for the
>>> coordinates?
>>>
>>> From the NAMD wiki:
>>>
>>> III. obtain a binary format representation of your coordinates. The
>>> coordinate output file of a non memory optimized run would work. Or extract
>>> the binary coordinates using VMD.
>>>
>>> IV. replace "coordinates" with "bincoordinates" and replace the
>>> reference to the pdb file with a file containing binary format coordinates.
>>> Thanks
>>>
>>
>>
>>
>> --
>> Aron Broom M.Sc
>> PhD Student
>> Department of Chemistry
>> University of Waterloo
>>
>>
>
>
>
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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