From: Carlos Sosa (sosa0006_at_r.umn.edu)
Date: Sun Jun 17 2012 - 11:24:50 CDT
Yes, exactly. I need to generate that bin file. Similar to the compressed
psf which is triggered by "genCompressedPsf on". The wiki is a little
obscure as to how to generate the pdb file that appears to be needed.
On Sun, Jun 17, 2012 at 11:10 AM, Aron Broom <broomsday_at_gmail.com> wrote:
> 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
>
>
-- 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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