From: Carlos Sosa (sosa0006_at_r.umn.edu)
Date: Sun Jun 17 2012 - 10:20:38 CDT
This file produces apoa1.psf.inter apoa1.psf.inter.bin only. Did I miss
to add anything else?
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
coordinates apoa1.pdb
bincoordinates apoa1-out.coor
temperature 300
seed 74269
genCompressedPsf 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
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
binaryoutput yes
On Sat, Jun 16, 2012 at 9:22 PM, Aron Broom <broomsday_at_gmail.com> wrote:
> 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
>
>
-- Carlos P Sosa, Ph.D. Computational Chemistry Consultant and Adjunct Assistant Professor *Biomedical Informatics and Computational Biology (BICB) * Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota, Walters Library # 509, 117 Pleasant Street, Minneapolis, MN 55455.
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