Re: memory-optimized version binary coordinates?

From: Aron Broom (broomsday_at_gmail.com)
Date: Sun Jun 17 2012 - 11:10:31 CDT

I see, I don't know anything about compressed psf, so I can't help out with
that aspect.

What I don't understand from this is:

bincoordinates apoa1-out.coor
outname ./apoa1-out.coor

you realize that bincoordinates is the input? Your file seems a bit
cyclical.

On Sun, Jun 17, 2012 at 11:20 AM, Carlos Sosa <sosa0006_at_r.umn.edu> wrote:

>
> 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.
>

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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